Repetitive Elements in Myriapoda: Genomic Diversity and Evolution

Repetitive Elements in Myriapoda: Genomic Diversity and Evolution | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Repetitive Elements in Myriapoda: Genomic Diversity and Evolution Dorine Merlat, Gemma Collins, Clément Schneider, Arnaud Kress, and 4 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8918891/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Background Transposable elements (TEs) are major drivers of genome evolution, yet their diversity and dynamics remain poorly characterized in many non-model animal lineages, including Myriapoda. The recent expansion of genomic resources in this group now enables comparative analyses, but TE annotation remains challenging due to heterogeneous assembly qualities and the complexity of repeat landscapes. Results We present a standardized comparative analysis of repetitive elements across 36 myriapod species, providing a comprehensive overview of TE abundance, composition, and activity. TE landscapes vary strongly among lineages, with TIR elements dominating most genomes, while LTR elements show lineage-specific expansions, particularly in several chilopods. Genome size correlates strongly with TE abundance in diplopods, whereas this relationship is weaker and more variable in chilopods, suggesting contrasting evolutionary dynamics across clades. Repeat divergence analyses further reveal signatures of recent TE activity, indicating that repeat-driven genome remodeling remains ongoing in myriapods. Conclusion Our results demonstrate that genome size evolution in Myriapoda reflects lineage-specific TE dynamics and highlight the importance of standardized annotation for cross-species comparisons. We additionally provide an automated workflow for repeat annotation and visualization, enabling reproducible large-scale analyses of repeatomes in non-model organisms, and make this workflow publicly available at: https://github.com/dorinemerlat/exogap . Repetitive element Transposable elements Myriapoda Genome evolution Annotation Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Background Myriapoda are a fascinating and relatively understudied group within the arthropod phylum, characterized by their segmented bodies and numerous legs. They play critical roles in soil and forest ecosystems, contributing significantly to soil aeration, decomposition, and nutrient and water cycling [ 1 , 2 ]. This diverse group comprises four classes: Chilopoda (centipedes), Diplopoda (millipedes), Pauropoda, and Symphyla (garden centipedes or pseudocentipedes). The Diplopoda class is the most diverse, with around 13,000 known species across 16 orders [ 3 , 4 ]. Millipedes are characterized by having two pairs of legs on most trunk segments, and although the name “millipede” suggests a thousand legs, most species have far fewer. However, the recently described species Eumillipes persephone reaches a record 330 segments and up to 1,306 legs, the highest number known in any animal [ 5 ]. They primarily feed on decaying plant matter, making them important decomposers that enhance soil quality and nutrient cycling [ 6 , 7 ]. Chilopods have one pair of legs per segment and are characterized by rapid movement. They range from 14 to 177 pairs of legs [ 8 ] and possess venomous forcipules, specialized claws used for predation [ 4 ]. This class includes over 3,000 known species divided into five orders [ 9 ] and is unique among myriapods for its carnivorous diet. The lesser-known classes, Pauropoda and Symphyla, are smaller and feature simpler segmentation patterns with fewer legs. Pauropoda have 12 partially fused segments with 8 to 11 pairs of legs, including a reduced first pair [ 10 ], and consist of about 990 known species in two orders [ 11 ]. They feed on fungus hyphae, spores, and plant tissue [ 4 ]. Symphyla, with 15 to 22 body segments but only 11 or 12 pairs of legs, contains roughly 200 known species in a single order [ 12 ]. They mainly feed saprophagous, but some species are also predators. These classes, although less diverse and less well studied, contribute to diverse ecological functions within their habitats. The diverse morphologies and ecological functions of myriapods underscore their ecological significance across various environments. Despite their importance, the exploration of myriapod genetics and genomics has historically lagged behind that of other arthropod groups, such as insects and crustaceans. However, recent advances in sequencing technologies have begun to bridge this gap. The first myriapod genome, that of Strigamia maritima , was sequenced in 2011 [ 13 ]. This was followed by the sequencing of the first diplopod genomes, Helicorthomorpha holstii and Trigoniulus corallinus [ 14 ]. An additional seven genomes of varying quality were provided by a 2020 study on myriapod genomics [ 15 ]. A major breakthrough in myriapod genomics came with the MetaInvert project, an international initiative that gathered genomic data from 232 invertebrate species, including 45 myriapods [ 16 ]. At the time of writing, the number of available myriapod genomes has increased to 68. In terms of genome size, most available myriapod assemblies range from 118.1 Mb to 800 Mb. Hovewer, seven species have genomes larger than 1 Gb, and four of them exceed 2 Gb: Agaricogonopus acrotrifoliolatus (2.2 Gb), Thereuonema tuberculata (2.4 Gb), Rhysida immarginata (2.5 Gb) and Lithobius niger (3.2 Gb) [ 15 ]. This marked variation suggests substantial differences in genome architecture, yet the underlying drivers—such as repetitive element accumulation—remain poorly characterized. The quality of genome assemblies varies considerably, with only 7 genomes assembled at the chromosomal level, while the others remain at the scaffold or contig level. The genomes of symphylans and pauropods are among the most fragmented. So, comprehensive genomic resources for myriapods remain scarce, and much of their genome architecture, including repetitive elements, remains largely unexplored. Repetitive elements (REs), long considered as non-functional "junk" DNA, are now recognized for their critical roles in genome organization, regulation, and evolution [ 17 ]. Beyond their significant influence on genome size, REs also shape the structure and drive the evolution of eukaryotic genomes. However, their repetitive nature poses substantial challenges for genome assembly and annotation [ 18 ], complicating their accurate identification and classification, and the understanding of their impact on host genomes. REs can be broadly categorized into two main types: transposable elements (TEs) and tandem repeats (TRs), each with distinct characteristics and biological functions. TEs, often referred to as "jumping genes," are DNA sequences capable of moving from one location to another within the genome, significantly impacting genomic stability and gene function. For example, they contribute to the regulation of gene expression by recruiting silencing machinery [ 19 ], which represses gene expression via epigenetic modifications. Additionally, TEs contribute to genome evolution by serving as origin of some microRNAs [ 20 ]. They are classified into two primary groups based on their transposition intermediate: RNA-mediated elements (class I, or retrotransposons) and DNA-mediated elements (class II, or DNA transposons) [ 21 , 22 ]. Class I TEs use a mechanism commonly called “copy and paste”. This process starts with the transcription of the DNA sequence into RNA, which is then reverse transcribed into DNA by a TE-encoded reverse transcriptase (RT) and inserted into a new genomic location [ 23 ]. They include Long Terminal Repeat (LTR), Non-LTR retrotransposons, DIRS-like elements, and Penelope-like elements (PLEs). LTR retrotransposons are defined by the presence of long repeated sequences at both ends. They resemble retroviruses and span from a few hundred to several thousand base pairs. Non-LTR retrotransposons distinguished by the absence of LTRs are organized into 2 orders: Long Interspersed Nuclear Elements (LINEs) and Short Interspersed Nuclear Elements (SINEs). Both LINEs and SINES possess a poly-A tail at the 3' end and are flanked by target site duplications. LINEs are autonomous retrotransposons that encode reverse transcriptase and are typically over 5 kb in length. In animal genomes, LINEs are abundant; for instance, 100 LINE subfamilies alone constitute approximately 3% of the malaria mosquito Anopheles gambiae genome [ 24 ]. SINEs are short (< 700 bp) non-autonomous retrotransposons that rely on LINE-encoded reverse transcriptase for their reverse transcription. SINEs play a role in genetic variation, providing regulatory elements for gene expression or alternative splice sites [ 25 ]. DIRS-like elements are a divergent group of retroelements that encode RT but differ by containing a Tyrosine recombinase (YR) gene instead of an integrase. The last group of retrotransposons, PLEs, have a single ORF that encodes a protein with both RT and endonuclease (EN) activities. The RT domain of PLEs is more similar to telomerase, than the RT from LTRs or LINEs. PLEs are absent from the genomes of mammals, birds, and Caenorhabditis elegans , though this absence may be due to a loss event [ 26 ]. The only active representative, Penelope, has been identified in Drosophila virilis , and its invasion appears to be relatively recent [ 27 ]. Due to their replication mechanism, which generates a new copy with each cycle, class I elements are the primary contributors to the repetitive fraction in large genomes [ 22 ]. Class II TEs move directly from one DNA location to another without involving an RNA intermediate. Depending on the number of DNA strands cleaved during transposition, they can be further classified into two subclasses: Terminal Inverted Repeat (TIR) and Cryptons belong to subclass I, while Mavericks (or Polintons) and Helitrons belong to subclass II. TIR are characterized by inverted repeat sequences at their ends and encode the transposase that binds near the inverted repeat to mediate mobility [ 27 ]. Cryptons, however, lack transposase and instead rely on a tyrosine recombinase for their movement. Initially identified in fungi, they have since been shown to be present in a broader range of species, including insects [ 28 ]. Helitrons and Mavericks use a rolling-circle mechanism to move and can capture and mobilize fragments of other genomic regions, thereby contributing to genetic diversity and genomic rearrangements [ 29 ]. Helitrons are found in plants, fungi and mammals [ 30 ], while Mavericks are large transposons commonly found in eukaryotic genomes, except for plants [ 31 ]. In addition to TEs, TRs represent another important aspect of genomic organization. These are DNA sequences in which units are repeated adjacently in a head-to-tail arrangement. They are categorized into several orders, including microsatellites, minisatellites, and satellites. Microsatellites, also known as Simple Sequence Repeats, are highly variable among individuals and populations, making them valuable for genetic mapping and population genetics studies. Additionally, microsatellites can influence gene function and contribute to genetic diversity. In contrast, minisatellites are longer and are often found in telomeric regions of the genome. They are associated with genomic instability and chromosomal rearrangements and can affect gene regulation and epigenetic modifications [ 32 ]. Satellites, the third class, are composed of even larger repeating units, ranging from a few hundred to several thousand base pairs. Satellites are typically located in centromeric and pericentromeric regions of chromosomes, where they play crucial roles in chromosome structure and segregation during cell division. Due to their repetitive nature and size, satellite DNA is often involved in maintaining chromosomal stability and can contribute to evolutionary changes in genome structure. Considering their significant roles, REs have been extensively studied in Arthropoda, particularly in insects [ 33 ] where their abundance greatly varies among orders and even between species belonging to the same order. In Diptera for example, the TE content ranges from less than 1% in Belgica antarctica to around 55% in the yellow fever mosquito Aedes aegypti . Even among closely related Drosophila species, the TE content ranges from 10% (in D. miranda and D. simulans ) to 40% (in D. ananassae ). The highest TE content (60%) was found in the large genome (6.5 Gb) of the migratory locust Locusta migratoria (Orthoptera). While most REs have been characterized in well-studied model species such as D. melanogaster , classification of REs is often difficult in non-model species. For example, unknown elements account for up to 93% of TEs in the mayfly Ephemera danica . Unlike insects, very little is known about the REs of myriapods. The first comparative study between three species [ 14 ] highlights the importance of LINEs and DNA transposons in the expansion of the T. corallinus genome, with TE coverage reaching 55%, whereas TEs represent only 19% of the H. holstii genome. This substantial variability seems to indicate that TEs are major players in the dynamics of Myriapod genomes. The aim of our study is to provide a comprehensive analysis of REs across a large range of myriapod species based on a standardized RE annotation protocol. Our annotation of REs in 37 genomes allowed us to characterize the diversity and respective abundance of the different families making up the myriapod repeatome. By comparing TE composition across species, we identified common patterns as well as lineage-specific variations, highlighting both conserved and divergent evolutionary trajectories. Furthermore, we examined the relationship between RE content and genome assembly size, revealing contrasting trends between Diplopoda and Chilopoda. Finally, through an analysis of TE landscapes and divergence patterns, we explored the evolutionary dynamics of REs in Myriapoda, shedding light on their role in genome plasticity and lineage diversification. Materials and methods Genomic datasets The myriapod genome assemblies were retrieved from the NCBI Genome database [ 34 ] in August 2025. Genomes were selected based on data quality by requiring a BUSCO (version 6.0.0) [ 35 ] completeness score above 70%, assessed using the Arthropoda OrthoDB v10 dataset [ 36 ], and a contig N50 greater than 5 kb (Table 1 ). Additionally, only one genome per species was retained based on the quality of the assembly, except for Strigamia acuminata . For this species, two genomes were included for comparison purposes: one provided by the Darwin Tree of Life project [ 37 , 38 ], assembled at the chromosomal level, and another by MetaInvert, assembled at the contig level. This selection process yielded a final dataset comprising 36 species (Fig. 1 ) and 37 genomes, including 16 Chilopoda and 20 Diplopoda species. Unfortunately, no genomes from Symphyla or Pauropoda met the quality criteria for inclusion in the analysis. Table 1 Genomic datasets used in this study. For Strigamia acuminata , two assemblies were retained: one assembled at the chromosomal level (chrom.) and the other at the contig level (cont.). Class Organism Name Assembly Accession Assembly level Assembly size (Mb) Contig N50 (kb) BUSCO -C (%) Ref. Chilopoda Cryptops parisi GCA_034695005.1 Contig 304 14.7 77.1 [ 16 ] Geophilus carpophagus GCA_034687075.1 Contig 141 8.0 82.7 [ 16 ] Geophilus flavus GCA_034695885.1 Contig 187 5.7 72.7 [ 16 ] Geophilus truncorum GCA_034695745.1 Contig 137 12.8 83.4 [ 16 ] Henia vesuviana GCA_034696185.1 Contig 148 5.4 80.8 [ 16 ] Lithobius niger GCA_023313725.1 Scaffold 3,238 15.4 70.4 [ 15 ] Lithobius variegatus GCA_965125955.1 Chromosome 1,767 2,691.4 98.6 [ 39 ] Pachymerium ferrugineum GCA_034686365.1 Contig 118 28.3 81.7 [ 16 ] Rhysida immarginata GCA_023313115.1 Scaffold 2,529 33.8 89.9 [ 15 ] Scolopendra cretica GCA_966189295.1 Chromosome 1,456 81,956.2 97.7 Stenotaenia linearis GCA_034700445.1 Scaffold 148 8.0 77.8 [ 16 ] Strigamia acuminata (chrom.) GCA_949358305.1 Chromosome 238 1,816.0 98.9 [ 37 ] Strigamia acuminata (cont.) GCA_034703045.1 Contig 131 11.5 77.2 [ 16 ] Strigamia crassipes GCA_034683725.1 Contig 131 14.2 77.8 [ 16 ] Strigamia maritima GCA_000239455.1 Scaffold 176 24.7 98 [ 13 ] Strigamia transsilvanica* GCA_034701245.1 Scaffold 124 12.4 71.5 [ 16 ] Thereuonema tuberculata GCA_023159025.1 Scaffold 2,458 23.0 91.6 [ 15 ] Diplopoda Agaricogonopus acrotrifoliolatus GCA_052040765.1 Chromosome 2,241 360,240.6 98.4 Brachycybe producta GCA_036925085.1 Scaffold 295 1,616.7 98.3 Choneiulus palmatus GCA_965278725.1 Chromosome 627 1,186.7 98.4 [ 40 ] Cylindroiulus punctatus GCA_034695085.1 Chromosome 354 1,367.8 98.5 [ 41 ] Glomeris maerens GCA_023279145.1 Scaffold 150 9.8 85.8 [ 15 ] Glomeris marginata GCA_034696005.1 Contig 163 9.0 71.7 [ 16 ] Helicorthomorpha holstii GCA_013389785.1 Scaffold 181 59.2 96.7 [ 14 ] Julidae sp. JJ-2019** GCA_023279205.1 Scaffold 613 15.4 89.9 [ 15 ] Julus scandinavius GCA_034696685.1 Contig 251 9.9 72.8 [ 16 ] Julus scanicus GCA_034698625.1 Contig 251 12.2 74.8 [ 16 ] Kryphioiulus occultus GCA_034687865.1 Contig 229 18.3 72.1 [ 16 ] Megaphyllum sjaelandicum GCA_034698745.1 Contig 333 9.9 73.7 [ 16 ] Nanogona polydesmoides GCA_965153395.1 Chromosome 406 781.0 98 [ 42 ] Ommatoiulus sabulosus GCA_034697705.1 Contig 334 9.5 73.1 [ 16 ] Platydesmidae sp. JHPL-2020** GCA_023159045.1 Scaffold 328 8.8 91.7 [ 15 ] Polydesmus complanatus GCA_034692225.1 Contig 164 29.8 82.6 [ 16 ] Proteroiulus fuscus GCA_034700285.1 Contig 259 7.4 73.8 [ 16 ] Rossiulus vilnensis GCA_034700785.1 Contig 211 19.1 73.9 [ 16 ] Trigoniulus corallinus GCA_013389805.1 Scaffold 449 54.3 97.8 [ 14 ] Xestoiulus laeticollis GCA_034698905.1 Contig 304 10.3 76.9 [ 37 ] *: the genome was originally published under the species name of S. transsilvanica , but following taxonomic revision, it has been reassigned to S. crassipes . **: P. sp. JHPL-2020 et J. sp. JJ-2019 are respectively referenced as Niponia nodulosa and Anaulaciulus tonginus in So et al. article [ 15 ]. Annotation of repetitive elements Identification of TEs De novo identification of REs was initially performed using RepeatModeler2 (version 2.0.3, with the options -LTRStruct and -engine ncbi ) [ 43 ] (Fig. 2 ). This software leverages tools such as LTRharvest (version 1.6.4) [ 44 ] and LTR_retriever (version 2.9.4) [ 45 ] to enhance the detection of LTR. All consensus families generated by RepeatModeler2 were then provided to MCHelper [ 46 ] (version 1.7.1 fully automated mode with -b arthropoda_odb10.hmm) for curation and refinement. MCHelper removes false positives such as consensus sequences corresponding to multicopy protein-coding genes or short TRs, extends incomplete consensus sequences using the BEE (Blast–Extract–Extend) algorithm, identifies conserved TE domains and characteristic structural features, and classifies previously uncharacterized consensus sequences using a combination of homology search, domain inference, and structural evaluation. Finally, libraries from all species were combined and clustered with the arthropoda section of the RepBase library (version 26.05, May 2021; 19,232 sequences in this section) [ 47 ] using CD-HIT-EST (version 4.7, options -c 0.95 -g 1 -n 10 -l 80 -aS 98 ). This process resulted in a final TE library, which was subsequently used for annotation of REs with RepeatMasker (version 4.1.2-p1) using the options -e ncbi -a -gccalc -norna -excln -s . TRs were annotated using RepBase and Tandem Repeat Finder (TRF) [ 48 ] integrated in RepeatMasker. The procedures described above are included in the module dedicated to REs of EXOGAP (EXotic Organism Genome Annotation Pipeline), a Nextflow pipeline (version 24.04.1) available on GitHub ( https://github.com/dorinemerlat/exogap ). Correlation between genome size and TE abundance To estimate the contribution of REs to myriapod genomes, we calculated TE coverage as the proportion of the genome occupied by TEs. Prior to coverage calculation, RepeatMasker annotations were filtered to exclude low-complexity sequences, and overlapping TE annotations were merged using bedtools merge [ 49 ] (version v2.31.1) to avoid biased estimates caused by overlapping intervals. TE load was defined as the total number of TE copies per genome. Relationships between TE load or TE coverage and genome assembly size or assembly contiguity (measured by N50) were assessed using both linear regression and Spearman rank correlation analyses. Statistical significance was considered at p < 0.05. These analyses were performed in R [ 50 ] using the lm function and the ggplot2 package [ 51 ] for data visualization. Additionally, we generated a heatmap using ggplot2 to compare TE composition across species. Heatmap visualization of TE composition Heatmaps comparing TE composition across species were generated in R using the package ComplexHeatmap (version 2.26.1) [ 52 ]. TE load and TE coverage values were log-transformed prior to visualization to enable comparison among species with large differences in repeat abundance. TE annotations classified as unknown were excluded from the heatmaps. Estimating TE age distribution using kimura distance To infer the relative age distribution of REs, we estimated sequence divergence using Kimura two-parameter distances, which consider differences in transition and transversion rates. These calculations were performed using the RepeatMasker helper scripts calcDivergenceFromAlign.pl and createRepeatLandscape.pl . The Kimura distance was computed between each TE copy and its respective consensus sequence, allowing us to infer TE age distributions across species. A peak at low Kimura distances indicates recent TE activity, whereas higher divergence values reflect older TE insertions subjected to genetic drift or mutation accumulation. TE landscapes were generated for each species to compare the dynamics of TE expansions using ggplot2 . Results Overview of the Myriapoda repeatome We conducted a standardized analysis of 37 Myriapoda genomes from 36 species. Using RepeatModeler2 and MCHelper, we identified de novo a total of 54,785 RE families with 54,8% successfully assigned to known RE families. TRs are present in all myriapod species (Fig. 3 ), though their proportions vary. In terms of total copy number, the centipedes T. tuberculata and Scolopendra cretica , contain the highest TR loads, with approximately 798,000 and 434,000 copies, respectively. However, when considering genome coverage, the highest proportions are found in the millipedes Brachycybe producta (3.44% TR coverage) and P. Complanatus (2.28%) . The analysis of TEs across Myriapoda species reveals substantial variations in TE abundance and composition (Fig. 3 ). TE coverage (defined as the proportion of the genome occupied by TEs) ranges from 16% in Polydesmus complanatus to 81% in A. acrotrifoliolatus , although P. complanatus is not the smallest genome analyzed. The number of TE copies (load) varies dramatically, from 0.14 million in Pachymerium ferrugineum to 8.78 million in L. niger , which is also the species with the largest genome among the species studied. Across all Myriapoda, TIR elements dominate in most genomes in terms of both load and coverage. LTR elements typically rank second in coverage across these genomes, while the importance of LINEs varies considerably between species. Within the Diplopoda class, the Julida order exhibits consistent TE coverage and load across species, with a notable abundance of TIR elements. In the other diplopod genomes, the composition and importance of the repeatome is more diverse with certain species having unique TE patterns compared with all the myriapod genomes studied. T. corallinus is the only species with a significant proportion of SINE elements (9% of TE coverage), far exceeding the next highest value of 2% in Choneiulus palmatus . Additionally, A. acrotrifoliolatus has the highest proportion of LINE elements (29.6% of TE coverage), followed by T. corallinus (28.1%), Julidae. sp. JJ 2019 (14%) and R. immarginata (13.6%). The Chilopoda class also exhibits substantial variability in TE composition. LINEs are present at low abundance in Geophilomorpha genomes, accounting for no more than 0.84% of TE coverage. This pattern suggests a possible loss of most LINE elements in Geophilomorpha. In some chilopods, including the two Lithobiomorpha genomes and R. immarginata , Maverick elements contribute substantially to the TE load, with ~ 89,000 copies in L. niger , ~ 39,000 copies in Lithobius variegatus , and ~ 38,000 copies in R. immarginata . Surprisingly, LTR elements occur in highly variable proportions across both diplopods and chilopods. In several species, they represent a substantial fraction of TE composition, notably in Cylindroiulus punctatus and S. maritima , where LTR elements account for 54.2% and 52.5% of the composition of the TE coverage, respectively. However, in most analyzed genomes, LTR elements constitute a much smaller fraction, typically representing less than 30% of the composition of the TE coverage, indicating that they are not the dominant TE order across Myriapoda. No clear association between LTR abundance and myriapod classes was detected, as high and low LTR proportions occur in both diplopods and chilopods. Comparison of the two available S. acuminata assemblies further illustrates the impact of assembly contiguity on LTR detection. The chromosome-level assembly shows substantially higher TE coverage than the contig-level assembly (58.3% versus 36.4%) and, to a lesser extent, a higher TE copy number (462,000 versus 351,000 copies). This difference is largely driven by increased recovery of LTR elements, whose genomic coverage rises from 7.5% to 28.0%. These results indicate that fragmented assemblies may substantially underestimate the contribution of long and nested elements such as LTR retrotransposons. TE composition The analysis of the repeatome composition in myriapod genomes reveals a remarkable diversity (Fig. 4 for the load and Supplementary Fig. 1 for the coverage), with almost all known TE superfamilies represented in at least one species. Only a small number of TE groups—including Casposons, Novosib, IR4, and SINE families lacking a canonical RNA polymerase III promoter or associated with tRNA and 5S RNA—remain undetected across all analyzed genomes, suggesting either true absence or extremely low abundance in Myriapoda. Several species exhibit globally darker vertical patterns in the heatmaps, indicating elevated TE representation across multiple TE groups. These patterns largely correspond to species with the largest genome assemblies, suggesting genome-wide TE accumulation rather than expansions restricted to particular TE families. At the superfamily and family levels, TE profiles reveal a shared backbone of repetitive elements across both Diplopoda and Chilopoda, suggesting the presence of a conserved ancestral TE repertoire in myriapods with lineage-specific quantitative variations. Despite substantial variation in genome size and TE composition among species, several TE groups remain consistently abundant across most analyzed genomes. Among class II elements, terminal inverted repeat (TIR) DNA transposons represent the most prevalent groups, particularly the CACTA, Mutator, hAT, PIF/Harbinger, and Tc1/Mariner superfamilies. Rolling-circle Helitrons and large DNA elements such as Mavericks are also widely distributed, although their abundance varies markedly among species. Overall, Helitrons and Mavericks are recurrent components of myriapod genomes, albeit generally contributing less than the dominant TIR elements. Among class I elements, LTR retrotransposons constitute a major component of TE repertoires in many species, with Gypsy elements being particularly abundant, alongside Copia, Bel-Pao, and several unclassified LTR groups. LINE elements, especially RTE and CR1/Jockey-related clades, are likewise widespread across taxa, although their relative genomic contributions differ substantially among lineages, indicating lineage-specific histories of expansion and retention. Beyond these highly represented superfamilies, clear compositional differences are observed between Diplopoda and Chilopoda, as well as within these groups. Within Diplopoda, and particularly among Julida, many TE families and superfamilies show comparable coverage patterns across species, and generally display TE repertoires dominated by DNA transposons, particularly TIR elements. This is consistent with shared evolutionary history and broadly similar TE dynamics within this clade. T. corallinus stands out with a high abundance of LINEs I R1 and RTE, and 5S – Deu-core rRNA-derived. Additional differences at the TE family level are presented in Supplementary Fig. 2 (load) and Supplementary Fig. 3 (coverage). Among Chilopoda, a common TE background is likewise evident, with LINEs, LTRs, and DNA transposons consistently present across all species. However, contrasts among the major clades are more pronounced than within Diplopoda, with notable differences observed between Scolopendromorpha, Geophilomorpha, and Scutigeromorpha. Although MITEs appear to be detected in only two genomes, MITE elements were in fact identified by MCHelper in all analyzed genomes. Under the Dfam classification scheme used here, these short non-autonomous elements are generally assigned to their parental TIR superfamilies rather than to a dedicated MITE category, which likely explains their apparent absence from most genomes in the compositional heatmap. Actually, MITE-related insertions range from a few thousand copies in many diplopods and Geophilomorpha centipedes (typically ~ 2,000–30,000 copies per genome) to markedly higher values in several lineages. Particularly high numbers are observed in Lithobiomorpha ( L. niger , ~ 165,000 copies; L. variegatus , ~ 96,000 copies), as well as in large chilopod genomes such as R. immarginata (~ 474,000 copies), T. tuberculata (~ 256,000 copies), and S. cretica (~ 120,000 copies). Elevated counts are also observed in some diplopods, including A. acrotrifoliolatus (~ 114,000 copies), T. corallinus (~ 64,000 copies), and Platydesmidae sp. JHPL 2020 (~ 84,000 copies). These patterns indicate that MITE amplification varies strongly among lineages and tends to be associated with genomes already enriched in DNA transposons, suggesting that MITE dynamics broadly follow those of their autonomous TIR partners rather than forming independent expansion patterns. The load of TE superfamilies detected in the chromosome-level versus the contig-level assembly of S. acuminata are comparable, except for the TIR PiggyBac elements and Maverick TEs. However, some families such as Gypsy Micropia (LTR) are found only in the chromosome-level assembly, while RTE ORTE LINEs elements are detected exclusively in the contig-level genome. This element has been identified in only a few genomes across both Chilopoda and Diplopoda, indicating it may be difficult to detect accurately. Contribution of TEs to myriapod genome size A clear distinction emerges in TE load between genomes smaller than 1 Gb and larger genomes (Fig. 3 ). While smaller genomes contain fewer than ~ 627,000 TE copies, larger genomes harbor several million copies, ranging from ~ 3.2 million in S. cretica to ~ 8.8 million in L. niger. To investigate the contribution of TEs to genome size, we tested for correlations between TE load, TE coverage and genome assembly size in Diplopoda and Chilopoda. In Diplopoda, we observed strong positive correlations between genome assembly size and both TE load (Spearman’s rank correlation, ρ = 0.91, p = 0) (Fig. 5 A) and TE coverage (Spearman’s rank correlation, ρ = 0.91, p = 0) (Fig. 5 B). These results suggest that TEs contribute significantly to genome size variation in this group. In contrast to Diplopoda, the relationship between TE content and genome size in Chilopoda is more complex. TE load shows a strong positive correlation with genome assembly size (Spearman’s rank correlation, ρ = 0.88, p < 0.001) (Fig. 5 C), whereas TE coverage is only moderately correlated (Spearman’s rank correlation, ρ = 0.77, p < 0.001) (Fig. 5 D), suggesting that TE coverage alone does not explain genome size variation in chilopods. In fact, the 11 Geophilimorpha assemblies, all smaller than 250 Mb, exhibit TE coverage ranging from 16.1 to 58.4%. Some of these small genomes exhibit TE coverage comparable to, or even exceeding, that of genomes larger than 1 Gb. For example, the chromosome-level assembly of S. acuminata (238 Mb) achieves a TE coverage of 58.4%, which is comparable to the 60.2% coverage of the chromosome-level assembly of L. variegatus and higher than the 48.7% coverage of T. tuberculata , which nevertheless have much larger genomes (1.767 and 2.529 Gb, respectively). These results suggest complex relationship between genome size and TE content across Chilopoda. Since assembly contiguity can affect the recovery of long and nested repeats (notably LTRs), we investigated whether TE coverage correlated with assembly contiguity (N50). Correlations are weak to moderate and vary among clades ( Supplementary Fig. 4 ), indicating that assembly fragmentation alone does not explain the observed variation in repeat content. Overall, our results highlight a variable contribution of TEs to genome size within Myriapoda and more specifically within Chilopoda. These differences between Diplopoda and Chilopoda suggest distinct dynamics in TE evolution and genome architecture across these taxa. To better understand these patterns, we next examined the evolutionary dynamics of TE families across species. Evolution of transposable elements To investigate TE evolutionary dynamics across Myriapoda, we examined TE sequence divergence using Kimura substitution level (repeat landscape) plots (Fig. 6 ). These profiles approximate the age distribution of TE copies within each genome and highlight lineage-specific episodes of transposition, including recent bursts (low divergence) and older waves of accumulation (higher divergence). Across Diplopoda, repeat landscapes are generally dominated by TIR elements and a substantial fraction of unclassified repeats (Unknown), with broadly similar, unimodal shapes peaking at intermediate divergence levels (roughly ~ 10–25%), consistent with older or more gradual accumulation rather than extreme very recent bursts. This shared pattern is particularly evident within Julidae, which display closely comparable distributions, suggesting conserved repeat dynamics within this lineage. However, a subset of diplopods stands out by showing stronger contributions of retrotransposons: LINE-rich profiles are especially evident in Julidae sp. jj 2019 , A. acrotrifoliolatus and T. corallinus . Species-specific signals are also apparent in several genomes. C. punctatus exhibits two distinct peaks associated with LTR elements, consistent with multiple past expansion events of these retrotransposons. Likewise, Nanogona polydesmoides exhibits two distinct peaks associated with Helitron elements, indicating past expansion events of rolling-circle transposons in this lineage. Similarly, H. holstii displays a clear low-divergence peak corresponding to Maverick elements, revealing a lineage-specific expansion of these large DNA transposons that is not observed at comparable levels in closely related taxa. In addition, a SINE peak at approximately 20% divergence is observed exclusively in T. corallinus , while C. punctatus shows evidence of a relatively recent expansion of PLE elements. Within Chilopoda, repeat landscapes are markedly more heterogeneous, revealing strong differences among orders and species. Several taxa show pronounced recent LTR retrotransposon expansions, with large peaks at very low divergence levels. This pattern is particularly striking in S. acuminata and S. maritima , both of which exhibit strong LTR-dominated signals consistent with recent or ongoing TE activity. The comparison between the two available assemblies of S. acuminata further shows that the chromosome-level assembly contains a much stronger low-divergence signal than the contig-level assembly, indicating improved recovery of recent repetitive insertions in the more contiguous genome assembly. Other Geophilomorpha species display broader divergence profiles with less pronounced recent peaks, suggesting either older accumulation or reduced recent TE activity relative to other chilopod groups. Nevertheless, species-level differences remain visible; for example, Strigamia crassipes shows increased contributions of Helitron elements in the intermediate divergence classes. Lithobiomorpha species display comparatively strong low-divergence signals involving several TE classes, including LINEs and large DNA elements, consistent with recent TE accumulation. For L. variegatus , we can observe a recent or sustained activity of Maverick elements. These patterns are in agreement with the high TE copy numbers observed in these large genomes and indicate active or recent TE proliferation in this lineage. Recent or ongoing expansions are also visible in the other large genomes of Chilopoda, namely T. tuberculata (Scutigeromorpha) and the Scolopendromorpha S. cretica and R. immarginata , with a predominant expansion of TIRs. Conversely, the Scolopendromorpha C. parisi , whose genome size is much smaller, shows very little recent activity. Overall, repeat landscapes reveal both group-level similarities and species-specific bursts of activity across Myriapoda. Diplopod genomes generally show more homogeneous and older TE accumulation patterns, whereas chilopod genomes display greater variability, with several lineages exhibiting strong recent TE expansions driven by distinct TE classes. These results highlight that TE evolutionary histories differ substantially among myriapod lineages and often involve lineage-specific expansions of particular TE families. Discussion Advantages of RE annotation approach The use of a unified and integrative annotation strategy enables comparisons of repeat composition across myriapod genomes, reducing methodological biases that often complicate cross-study interpretations. Importantly, applying a standardized annotation workflow across all analyzed genomes produces harmonized annotation files and analytical outputs, facilitating reproducible comparison. The EXOGAP framework relies on de novo repeat discovery using RepeatModeler2, followed by systematic refinement of repeat libraries using MCHelper prior to genome masking. This strategy is particularly valuable for non-model organisms, where repeat diversity is often poorly represented in existing databases and assemblies may remain fragmented. MCHelper refines de novo libraries by identifying gene-related sequences that may otherwise be retained as repeats, thereby reducing potential false positives. In addition, it integrates similarity searches, conserved domain detection, and structural characteristics to improve repeat classification. This refinement step also frequently extends consensus sequences predicted by RepeatModeler2, resulting in more complete repeat families and improving downstream genome annotation. In particular, the refined libraries enable a clearer distinction between different orders within Class II transposable elements. By improving the consistency and resolution of repeat classification, our approach provides a more detailed view of repeat composition across myriapod genomes. To date, few studies have focused on the REs of myriapods. Petersen et al. [ 33 ], in their pioneering comparative study on arthropods, analyzed 73 arthropod genomes, primarily from insects (62 genomes), with only 11 genomes from other arthropod groups. This study was the first to include a myriapod genome ( S. maritima ). Qu et al. [ 14 ] conducted the first comparative genomic study focusing exclusively on myriapods, analyzing the first three available myriapod genomes: S. maritima , H. holstii , and T. corallinus . A second comparative genomic study was conducted by So et al. [ 15 ], comprising six additional genomes. Compared to the classical RepeatModeler–RepeatMasker approach used in these pioneering studies, the combination of RepeatModeler and MCHelper for library construction improves the classification of repetitive elements (Fig. 7 ). Across most genomes examined, repeat annotations obtained here result in higher estimates of total TE coverage compared with previous studies, often accompanied by a reduction in the proportion of unclassified elements. However, the most notable improvement concerns the identification of specific TE. In particular, Class II DNA transposons and LTR retrotransposons are consistently recovered at substantially higher levels than previously reported, sometimes revealing several-fold increases in coverage. Impact of technical limitations on results Identifying and accurately annotating TEs remains a significant challenge, particularly in fragmented genome assemblies. These differences are illustrated by the comparison between two S. acuminata assemblies: a fragmented assembly obtained from Illumina reads and a chromosome-level assembly based on long read sequencing. The chromosome-level assembly shows only a slightly higher TE load (0.46 million copies compared with 0.35 million in the contig-level assembly), and the relative contributions of the different repeat orders remain broadly similar between assemblies. In contrast, TE coverage differs markedly, increasing from 35.4% in the contig-level assembly to 58.4% in the chromosome-level assembly. This indicates that although our approach efficiently detects the presence and diversity of TE families, many copies remain fragmented in lower-quality assemblies and therefore do not fully contribute to coverage estimates. More generally, the significant "unclassified" proportion of TEs in assemblies, including chromosome-level assemblies, underscores the ongoing challenges associated with TE classification in non-model species, potentially obscuring the true genomic contributions of DNA transposons, LTRs, LINEs, and SINEs. An additional challenge arises from the difficulty of accurately assembling satellite DNA. These regions are notoriously difficult to assemble, particularly in genomes sequenced with short-read technologies. Consequently, the relative contribution of satellite DNA to the overall genomic landscape is difficult to estimate. These findings emphasize the need for improved assembly strategies and annotation methods to achieve a more comprehensive characterization of TEs and satellite DNAs, especially in fragmented genomes. Key findings in TE dynamics across Myriapoda species Our study highlights the significant variation in TE abundance, composition, and contribution to genome size across Myriapoda species. While TIR and LTR elements dominate the genomes of most Myriapoda species, some species, particularly those with large genomes, are also rich in LINEs. For instance, LINEs account for 29.6% of the A. acrotrifoliolatus genome. Within the Diplopoda, we observe relatively consistent TE compositions, especially within the Julida group, which share a similar evolutionary history, resulting in comparable TE profiles across species. However, certain Diplopoda species exhibit distinctive TE profiles. T. corallinus is characterized by a high proportion of SINEs (9% of TE coverage), showing unique evolutionary trajectories compared to other Myriapoda species. Meanwhile, H. holstii exhibits an increased presence of Maverick elements. This pattern contrasts with the broader diversity seen in Chilopoda, where TE compositions are more variable, influenced by both TIR and LTR elements. Recent or ongoing expansions of TIR elements are especially important in the large genomes of Scolopendromorpha, while recent bursts of LTR elements play a key role in species such as S. maritima and S. acuminata . This variation in TE composition suggests that the dynamics of REs may be shaped by distinct evolutionary pressures within different Myriapoda subgroups. Notably, genome size is strongly correlated with both TE load and TE coverage in Diplopoda, reflecting the expected pattern of larger genomes harboring more TEs. In contrast, Chilopoda exhibits more complex relationships, with genome size strongly correlated to TE load but moderately with TE coverage. Indeed, species like S. acuminata and S. maritima display comparable or even greater TE coverage than larger genomes like those of L. variegatus and T. tuberculata. This may be attributed to the recent expansion of LTR elements in these two Strigamia species. More broadly, our study highlights the variability of TE dynamics across Myriapods, and particularly within Chilopoda, with the genomes of some species being shaped by recent or ongoing TE expansions. This may suggest lineage-specific shifts in TE regulation, recent TE invasion mediated by horizontal transfer or demographic factors limiting the efficiency of purifying selection against newly inserted elements in some species. The repeatome analysis revealed that nearly all known TE superfamilies are represented across Myriapoda species, though their abundance varies significantly. For example, the DIRS superfamily is more abundant in Chilopoda, while RTE elements are more prominent in Diplopoda. Several relatively rare families or subfamilies (e.g., Helitron, Penelope, and various groups related to MITE/Kolobok/Ginger/Zator) display mosaic distributions across species. Such patterns may reflect very recent lineage-specific activity, multiple independent losses, or limitations in the assignment of highly divergent TEs. These families therefore represent promising candidates for dedicated analyses (e.g., transposase or reverse transcriptase phylogenies, insertion dating) aimed at disentangling the underlying evolutionary scenarios. Comparison with other arthropod groups There is no clear pattern of conservation of REs across the entire arthropod clade, making comparisons challenging. The lack of a standardized classification of REs further complicates direct comparisons between species and groups. However, our study highlights the remarkable diversity in the distribution of REs in myriapods, which aligns with previous findings in other arthropods [ 53 ]. We show that myriapod genomes present a rich diversity of TE families, with few entirely absent: Casposons, typically confined to bacteria and archaea [ 54 ]; IR4 elements, documented solely in Caenorhabditis elegans; VIPER elements [ 55 ], associated with Kinetoplastids and notably, Novosib elements, identified exclusively in certain insect species. Interestingly, SINE retrotransposons present across all Insect orders [ 33 ] are largely absent in myriapods, with the notable exception of T. corallinus . We observed notable differences in TE coverage and composition between Myriapods and other Arthropods. Myriapods exhibit a TE coverage ranging from 16% to 81% which is higher than that of chelicerates, where TE coverage does not exceed 40% [ 33 ]. However, this coverage is lower compared to certain crustaceans with large genomes; for instance, the genome of Paralithodes platypus (4.8 Gb) has a TE coverage of 78.89% [ 56 ]. Moreover, myriapod genomes are primarily characterized by a strong contribution of DNA transposons, particularly terminal inverted repeat (TIR) elements, which dominate TE composition in most analyzed species. In contrast, Class I retrotransposons, especially LTR elements, show highly variable contributions and become prominent only in certain lineages, notably among some chilopods, without consistently dominating TE repertoires across the group. This pattern differs not only from many insect genomes, where LINEs or LTR retrotransposons frequently constitute the largest TE fractions, but also from chelicerates. In chelicerates, TE composition appears highly heterogeneous across species, with no consistent dominance of a single TE class, although DNA transposons often represent an important component. By contrast, myriapods display a more consistent predominance of TIR elements across species, suggesting more homogeneous large-scale TE dynamics within the group. Together, these observations indicate that myriapods possess a distinctive TE landscape in which DNA transposons and lineage-specific retrotransposon expansions jointly shape genome architecture. This combination likely contributes to the diversity of genome sizes and evolutionary trajectories observed across Myriapoda. Future prospects Advancing our understanding of TEs in Myriapoda and other arthropods faces several challenges. A significant limitation is the persistent presence of unclassified REs which underscores the need for improved TEs classification techniques. One potential solution lies in integrating advanced computational tools, such as machine learning approaches like DeepTE [ 57 ], TEClass2 [ 58 ], Terrier [ 59 ], TERL [ 60 ], and the newer framework CREATE [ 61 ] show promise by learning sequence features beyond similarity-based methods. However, these approaches generally rely on training datasets that do not fully capture the diversity of transposable elements across taxa, which can limit classification accuracy for highly divergent or lineage-specific repeats [ 59 ]. Moreover, some tools assign only broad TE classes unless retrained on user-provided data. As these methods are still relatively recent, broader validation across diverse genomes will be necessary, and classification of degraded or poorly characterized repeats remains challenging. Another crucial step is to expand genomic databases such as Dfam [ 62 ]. Although Dfam now includes thousands of species, representation remains uneven across major taxonomic groups — notably, Myriapoda are not yet represented in this database. Increasing the availability of high-quality genome assemblies, particularly those generated with long-read sequencing technologies, represents another important research avenue. Long-read assemblies enable the detection of approximately 36% more REs compared to short-read technologies, with LTRs showing a remarkable 162% increase in detection rates [ 63 ]. Efforts to generate such assemblies are essential for improving TE characterization. Addressing taxonomic gaps in genomic data is equally critical. The Symphyla and Pauropoda classes of Myriapoda, for instance, remain unrepresented in current genomic studies. Generating high-quality genome assemblies for these groups would not only fill this gap but also provide a more complete picture of TE diversity and dynamics within Myriapoda. This, in turn, would lay the groundwork for broader comparative analyses. Expanding the scope of research to include a wider range of arthropod genomes would further enhance our understanding of lineage-specific trends and evolutionary patterns in TEs. Moreover, adopting a standardized analytical framework across studies would enable more meaningful comparisons and facilitate the identification of both shared features and unique adaptations across taxa, ultimately advancing the field significantly. Abbreviations Cont. contig Chrom. chromosome EXOGAP Exotic Organism Genome Annotation Pipeline LINE Long Interspersed Nuclear Elements LTR Long Terminal Repeat PLE Penelope like Element RE Repetitive Elements TE Transposable Element TIR Terminal Inverted Repeat TR Tandem Repeat SINE Short Interspersed Nuclear Elements Declarations Ethics approval and consent to participate Not applicable. Consent for publication Not applicable. Competing interests The authors declare no competing interests. Funding DM was supported by the French ministry of higher education and research and the doctoral school of Life Science of the University of Strasbourg. GC, CS, RL MB were supported through Landes-Offensive zur Entwicklung Wissenschaftlich-ökonomischer Exzellenz (LOEWE) Program of the Hessian Ministry of Higher Education, Research, Science and the Arts through the LOEWE/1/10/519/03/03.001(0014)/52 project (LOEWE Centre for Translational Biodiversity Genomics - LOEWE-TBG). Author Contribution OL and MB designed the study. GM, CS, PD, RL and MB generated much of the genomic data used in this study. DM and AK developed the annotation pipeline. DM analyzed the data. DM and OL interpreted data. DM and OL drafted the work and JT revised it. All authors reviewed the manuscript and agreed to the content. Acknowledgement We thank the members of the BiGEst-ICube platform for their assistance and the Soil Invertebrate Genome Initiative (SIGI) (https://tbg.senckenberg.de/sigi/) consortium for helpful discussions. Data Availability The EXOGAP pipeline is publicly available on GitHub at [https://github.com/dorinemerlat/exogap](https:/github.com/dorinemerlat/exogap) . Genome assemblies analyzed in this study are available on NCBI Genomes database, with accession numbers provided in Materials and Methods. The *de novo* TE libraries and corresponding annotation files generated in this study have been deposited in Zenodo (https://doi.org/10.5281/zenodo.18695040). References Marek PE, Shear WA, Myriapods. Curr Biol. 2022;32:R1294–6. https://doi.org/10.1016/j.cub.2022.09.058 . European Commission. Joint Research Centre. Global soil biodiversity atlas. LU: Publications Office; 2016. https://doi.org/10.2788/799182 . Sierwald P, Bond JE. Current Status of the Myriapod Class Diplopoda (Millipedes): Taxonomic Diversity and Phylogeny. Annu Rev Entomol. 2007;52:401–20. https://doi.org/10.1146/annurev.ento.52.111805.090210 . Minelli A. The Myriapoda: Treatise on Zoology - Anatomy, Taxonomy, Biology. 1st ed. Leiden: BRILL; 2011. Marek PE, Buzatto BA, Shear WA, Means JC, Black DG, Harvey MS, et al. The first true millipede—1306 legs long. Sci Rep. 2021;11:23126. https://doi.org/10.1038/s41598-021-02447-0 . Tóth Z, Hornung E. Taxonomic and Functional Response of Millipedes (Diplopoda) to Urban Soil Disturbance in a Metropolitan Area. Insects. 2019;11:25. https://doi.org/10.3390/insects11010025 . Joly F-X, Coq S, Coulis M, David J-F, Hättenschwiler S, Mueller CW, et al. Detritivore conversion of litter into faeces accelerates organic matter turnover. Commun Biol. 2020;3:660. https://doi.org/10.1038/s42003-020-01392-4 . Undheim EAB, King GF. On the venom system of centipedes (Chilopoda), a neglected group of venomous animals. Toxicon. 2011;57:512–24. https://doi.org/10.1016/j.toxicon.2011.01.004 . Edgecombe GD, Giribet G. Evolutionary Biology of Centipedes (Myriapoda: Chilopoda). Annu Rev Entomol. 2007;52:151–70. https://doi.org/10.1146/annurev.ento.52.110405.091326 . Scheller U. A reclassification of the Pauropoda (Myriapoda). Int J Myriapodology. 2008;1:1–38. https://doi.org/10.1163/187525408X316730 . Gao Y, Bu Y. Two new species of the genus Samarangopus and the first record of Eurypauropus japonicus (Arthropoda, Myriapoda, Pauropoda, Eurypauropodidae) from China. ZK. 2023;1165:137–54. https://doi.org/10.3897/zookeys.1165.102936 . Brewer MS, Sierwald P, Bond JE. Millipede Taxonomy after 250 Years: Classification and Taxonomic Practices in a Mega-Diverse yet Understudied Arthropod Group. PLoS ONE. 2012;7:e37240. https://doi.org/10.1371/journal.pone.0037240 . Chipman AD, Ferrier DEK, Brena C, Qu J, Hughes DST, Schröder R, et al. The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima. PLoS Biol. 2014;12:e1002005. https://doi.org/10.1371/journal.pbio.1002005 . Qu Z, Nong W, So WL, Barton-Owen T, Li Y, Leung TCN, et al. Millipede genomes reveal unique adaptations during myriapod evolution. PLoS Biol. 2020;18:e3000636. https://doi.org/10.1371/journal.pbio.3000636 . So WL, Nong W, Xie Y, Baril T, Ma H, Qu Z, et al. Myriapod genomes reveal ancestral horizontal gene transfer and hormonal gene loss in millipedes. Nat Commun. 2022;13:3010. https://doi.org/10.1038/s41467-022-30690-0 . Collins G, Schneider C, Boštjančić LL, Burkhardt U, Christian A, Decker P, et al. The MetaInvert soil invertebrate genome resource provides insights into below-ground biodiversity and evolution. Commun Biol. 2023;6:1241. https://doi.org/10.1038/s42003-023-05621-4 . Biscotti MA, Olmo E, Heslop-Harrison JS. Repetitive DNA in eukaryotic genomes. Chromosome Res. 2015;23:415–20. https://doi.org/10.1007/s10577-015-9499-z . Tørresen OK, Star B, Mier P, Andrade-Navarro MA, Bateman A, Jarnot P, et al. Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases. Nucleic Acids Res. 2019;47:10994–1006. https://doi.org/10.1093/nar/gkz841 . Underwood CJ, Henderson IR, Martienssen RA. Genetic and epigenetic variation of transposable elements in Arabidopsis. Curr Opin Plant Biol. 2017;36:135–41. https://doi.org/10.1016/j.pbi.2017.03.002 . Qin S, Jin P, Zhou X, Chen L, Ma F. The Role of Transposable Elements in the Origin and Evolution of MicroRNAs in Human. PLoS ONE. 2015;10:e0131365. https://doi.org/10.1371/journal.pone.0131365 . Wicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, et al. A unified classification system for eukaryotic transposable elements. Nat Rev Genet. 2007;8:973–82. https://doi.org/10.1038/nrg2165 . Makałowski W, Gotea V, Pande A, Makałowska I. Transposable Elements: Classification, Identification, and Their Use As a Tool For Comparative Genomics. In: Anisimova M, editor. Evolutionary Genomics. New York, NY: Springer New York; 2019. pp. 177–207. https://doi.org/10.1007/978-1-4939-9074-0_6 . Havecker ER, Gao X, Voytas DF. The diversity of LTR retrotransposons. Genome Biol. 2004;5:225. https://doi.org/10.1186/gb-2004-5-6-225 . Biedler J. Non-LTR Retrotransposons in the African Malaria Mosquito, Anopheles gambiae: Unprecedented Diversity and Evidence of Recent Activity. Mol Biol Evol. 2003;20:1811–25. https://doi.org/10.1093/molbev/msg189 . Mills RE, Bennett EA, Iskow RC, Devine SE. Which transposable elements are active in the human genome? Trends Genet. 2007;23:183–91. https://doi.org/10.1016/j.tig.2007.02.006 . Arkhipova IR. Distribution and Phylogeny of Penelope-Like Elements in Eukaryotes. Syst Biol. 2006;55:875–85. https://doi.org/10.1080/10635150601077683 . Poulter RTM, Butler MI. Tyrosine Recombinase Retrotransposons and Transposons. Microbiol Spectr. 2015;3. https://doi.org/10.1128/microbiolspec.MDNA3-0036-2014 . 3.2.07. Kojima KK, Jurka J. Crypton transposons: identification of new diverse families and ancient domestication events. Mob DNA. 2011;2:12. https://doi.org/10.1186/1759-8753-2-12 . Thomas J, Pritham EJ. Helitrons, the Eukaryotic Rolling-circle Transposable Elements. Microbiol Spectr. 2015;3. https://doi.org/10.1128/microbiolspec.MDNA3-0049-2014 . 3.4.03. Pritham EJ, Feschotte C. Massive amplification of rolling-circle transposons in the lineage of the bat Myotis lucifugus. Proc Natl Acad Sci USA. 2007;104:1895–900. https://doi.org/10.1073/pnas.0609601104 . Pritham EJ, Putliwala T, Feschotte C. Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses. Gene. 2007;390:3–17. https://doi.org/10.1016/j.gene.2006.08.008 . Hannan AJ. Expanding horizons of tandem repeats in biology and medicine: Why ‘genomic dark matter’ matters. Emerg Top Life Sci. 2023;7:239–47. https://doi.org/10.1042/ETLS20230075 . Petersen M, Armisén D, Gibbs RA, Hering L, Khila A, Mayer G, et al. Diversity and evolution of the transposable element repertoire in arthropods with particular reference to insects. BMC Evol Biol. 2019;19:11. https://doi.org/10.1186/s12862-018-1324-9 . Schoch CL, Ciufo S, Domrachev M, Hotton CL, Kannan S, Khovanskaya R, et al. NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database. 2020;2020:baaa062. https://doi.org/10.1093/database/baaa062 . Tegenfeldt F, Kuznetsov D, Manni M, Berkeley M, Zdobnov EM, Kriventseva EV. OrthoDB and BUSCO update: annotation of orthologs with wider sampling of genomes. Nucleic Acids Res. 2025;53:D516–22. https://doi.org/10.1093/nar/gkae987 . Kriventseva EV, Kuznetsov D, Tegenfeldt F, Manni M, Dias R, Simão FA, et al. OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs. Nucleic Acids Res. 2019;47:D807–11. https://doi.org/10.1093/nar/gky1053 . Edgecombe GD, Sivell D et al. Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective,. The genome sequence of the centipede Strigamia acuminata (Leach, 1816). Wellcome Open Res. 2023;8:420. https://doi.org/10.12688/wellcomeopenres.19941.1 The Darwin Tree of Life Project Consortium, Blaxter M, Mieszkowska N, Di Palma F, Holland P, Durbin R, et al. Sequence locally, think globally: The Darwin Tree of Life Project. Proc Natl Acad Sci USA. 2022;119:e2115642118. https://doi.org/10.1073/pnas.2115642118 . Edgecombe GD, Crowley LM, Telfer MG, Hughes L et al. University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab,. The genome sequence of the banded centipede, Lithobius variegatus Leach, 1814. Wellcome Open Res. 2025;10:285. https://doi.org/10.12688/wellcomeopenres.24329.1 Gregory J, Edgecombe S et al. GD, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding Collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations,. The genome sequence of the millipede, Choneiulus palmatus (Nĕmec, 1895) (Julida: Blaniulidae). Wellcome Open Res. 2025;10:513. https://doi.org/10.12688/wellcomeopenres.24885.1 Edgecombe GD, Crowley LM, Telfer MG et al. University of Oxford and Wytham Woods Genome Acquisiiton Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team,. The genome sequence of the club-tailed millipede, Cylindroiulus punctatus (Leach, 1816). Wellcome Open Res. 2025;10:256. https://doi.org/10.12688/wellcomeopenres.24251.1 Owen C, Sivell O, Sivell D, Twitchett RJ, Edgecombe GD et al. Natural History Museum Genome Acquisition Lab,. The genome sequence of the eyed flat-backed millipede, Nanogona polydesmoides (Leach, 1814). Wellcome Open Res. 2025;10:332. https://doi.org/10.12688/wellcomeopenres.24341.1 Flynn JM, Hubley R, Goubert C, Rosen J, Clark AG, Feschotte C, et al. RepeatModeler2 for automated genomic discovery of transposable element families. Proc Natl Acad Sci USA. 2020;117:9451–7. https://doi.org/10.1073/pnas.1921046117 . Ellinghaus D, Kurtz S, Willhoeft U. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics. 2008;9:18. https://doi.org/10.1186/1471-2105-9-18 . Ou S, Jiang N, LTR_retriever:. A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons. Plant Physiol. 2018;176:1410–22. https://doi.org/10.1104/pp.17.01310 . Orozco-Arias S, Sierra P, Durbin R, González J. MCHelper automatically curates transposable element libraries across eukaryotic species. Genome Res. 2024;34:2256–68. https://doi.org/10.1101/gr.278821.123 . Bao W, Kojima KK, Kohany O. Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob DNA. 2015;6:11. https://doi.org/10.1186/s13100-015-0041-9 . Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27:573–80. https://doi.org/10.1093/nar/27.2.573 . Quinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841–2. https://doi.org/10.1093/bioinformatics/btq033 . R Core Team. R: a language and environment for statistical computing. manual. Vienna, Austria: R Foundation for Statistical Computing; 2021. Wickham H. ggplot2: Elegant Graphics for Data Analysis. New York, NY: Springer New York; 2009. https://doi.org/10.1007/978-0-387-98141-3 . Gu Z, Eils R, Schlesner M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics. 2016;32:2847–9. https://doi.org/10.1093/bioinformatics/btw313 . Wu C, Lu J. Diversification of Transposable Elements in Arthropods and Its Impact on Genome Evolution. Genes. 2019;10:338. https://doi.org/10.3390/genes10050338 . Krupovic M, Béguin P, Koonin EV. Casposons: mobile genetic elements that gave rise to the CRISPR-Cas adaptation machinery. Curr Opin Microbiol. 2017;38:36–43. https://doi.org/10.1016/j.mib.2017.04.004 . Lorenzi HA, Robledo G, Levin MJ. The VIPER elements of trypanosomes constitute a novel group of tyrosine recombinase-enconding retrotransposons. Mol Biochem Parasitol. 2006;145:184–94. https://doi.org/10.1016/j.molbiopara.2005.10.002 . Rutz C, Bonassin L, Kress A, Francesconi C, Boštjančić LL, Merlat D, et al. Abundance and Diversification of Repetitive Elements in Decapoda Genomes. Genes. 2023;14:1627. https://doi.org/10.3390/genes14081627 . Yan H, Bombarely A, Li S. DeepTE: a computational method for de novo classification of transposons with convolutional neural network. Bioinformatics. 2020;36:4269–75. https://doi.org/10.1093/bioinformatics/btaa519 . Bickmann L, Rodriguez M, Jiang X, Makalowski W. TEclass2: Classification of transposable elements using Transformers. 2023. https://doi.org/10.1101/2023.10.13.562246 Turnbull R, Young ND, Tescari E, Skerratt LF, Kosch TA. Terrier: a deep learning repeat classifier. Brief Bioinform. 2025;26:bbaf442. https://doi.org/10.1093/bib/bbaf442 . Da Cruz MHP, Domingues DS, Saito PTM, Paschoal AR, Bugatti PH. TERL: classification of transposable elements by convolutional neural networks. Brief Bioinform. 2021;22:bbaa185. https://doi.org/10.1093/bib/bbaa185 . Qi Y, Chen Y, Wu Y, Guo Y, Gao M, Zhang F, et al. CREATE: a novel attention-based framework for efficient classification of transposable elements. Brief Bioinform. 2025;26:bbaf608. https://doi.org/10.1093/bib/bbaf608 . Hubley R, Finn RD, Clements J, Eddy SR, Jones TA, Bao W, et al. The Dfam database of repetitive DNA families. Nucleic Acids Res. 2016;44:D81–9. https://doi.org/10.1093/nar/gkv1272 . Sproul JS, Hotaling S, Heckenhauer J, Powell A, Marshall D, Larracuente AM, et al. Analyses of 600 + insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges. Genome Res. 2023;33:1708–17. https://doi.org/10.1101/gr.277387.122 . Additional Declarations No competing interests reported. Supplementary Files supplementarytable1.csv supplementaryfigure4.pdf supplementaryfigure1.pdf supplementaryfigure3.pdf supplementaryfigure2.pdf Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-8918891","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":598853728,"identity":"59701824-ab37-4262-b7d2-cf86b77a8bb4","order_by":0,"name":"Dorine Merlat","email":"","orcid":"","institution":"University of Strasbourg","correspondingAuthor":false,"prefix":"","firstName":"Dorine","middleName":"","lastName":"Merlat","suffix":""},{"id":598853729,"identity":"fe9b10b7-780b-41e4-8f1d-af3dec52f5da","order_by":1,"name":"Gemma Collins","email":"","orcid":"","institution":"LOEWE Centre for Translational Biodiversity Genomics","correspondingAuthor":false,"prefix":"","firstName":"Gemma","middleName":"","lastName":"Collins","suffix":""},{"id":598853730,"identity":"ce5fd01d-51c7-400a-8fc2-79672cef953b","order_by":2,"name":"Clément Schneider","email":"","orcid":"","institution":"LOEWE Centre for Translational Biodiversity Genomics","correspondingAuthor":false,"prefix":"","firstName":"Clément","middleName":"","lastName":"Schneider","suffix":""},{"id":598853731,"identity":"2afb3ec5-4563-4d5d-858e-54fe6e4b1579","order_by":3,"name":"Arnaud Kress","email":"","orcid":"","institution":"University of Strasbourg","correspondingAuthor":false,"prefix":"","firstName":"Arnaud","middleName":"","lastName":"Kress","suffix":""},{"id":598853732,"identity":"7500c409-78da-40da-9c31-f95f6ca384c7","order_by":4,"name":"Peter Decker","email":"","orcid":"","institution":"LOEWE Centre for Translational Biodiversity Genomics","correspondingAuthor":false,"prefix":"","firstName":"Peter","middleName":"","lastName":"Decker","suffix":""},{"id":598853733,"identity":"96bff3d7-3c97-4325-a306-b3617d4fd219","order_by":5,"name":"Julie Thompson","email":"","orcid":"","institution":"University of Strasbourg","correspondingAuthor":false,"prefix":"","firstName":"Julie","middleName":"","lastName":"Thompson","suffix":""},{"id":598853734,"identity":"6ea168df-ca6e-4399-bf84-497ed41b55af","order_by":6,"name":"Miklós Bálint","email":"","orcid":"","institution":"LOEWE Centre for Translational Biodiversity Genomics","correspondingAuthor":false,"prefix":"","firstName":"Miklós","middleName":"","lastName":"Bálint","suffix":""},{"id":598853735,"identity":"083e6bbf-d153-4d52-81f5-15ae2509beb4","order_by":7,"name":"Odile Lecompte","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAABDklEQVRIie3Pv2vCQBTA8SeF3BK49Qn98S8kOLRD6N/iIdjJPYO07yjooO1s/4tMSreTgF1SXQsuCQ5d7VIcRLwkFRy8dC30vkPyLuQD7wBstj+ZkArg5nAKAM7KiVcQ0gTLWUE7JzXSc52MpAnHJM5f1YSzFqk14CXvD9qrdbgQE8Y+V2EX8Npg6sOMpiPABibvE08lS/H66PoymQGeq9PE+xAUu4Aiws4Yp72liGK3JsmBezQsVpAt4ENJdnNNWCZpB1hJ9PWbXkFIaQK+lD0zKe4y9NAf5XdJZq2GXsx/kc9oJJzdZekmDK54/2mcht3bi2jxln7Rd2AkP+sVT+f4UzU45Pz+i81ms/3L9m7AYbQgh+SQAAAAAElFTkSuQmCC","orcid":"","institution":"University of Strasbourg","correspondingAuthor":true,"prefix":"","firstName":"Odile","middleName":"","lastName":"Lecompte","suffix":""}],"badges":[],"createdAt":"2026-02-19 15:44:04","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-8918891/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-8918891/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":103941582,"identity":"7bc43216-8059-4906-a448-ee5d5c7228b3","added_by":"auto","created_at":"2026-03-04 19:27:56","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":1138673,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003ePhylogeny of Myriapoda species included in this study, based on the NCBI Taxonomy\u003c/strong\u003e [34]\u003cstrong\u003e.\u003c/strong\u003e The phylogeny highlights species from the classes Chilopoda and Diplopoda. Abbreviations: Spiros.: Spirostreptida; Spirob.: Spirobolida; Chord.: Chordeumatida; Scut.: Scutigeromorpha; Noto.: Notostigmophora; Cryt.: Cryptopidae; Dign: Dignathodontidae. Picture credits: Turner Brockman –\u003cem\u003e Brachycybe petasata (\u003c/em\u003ePlatydesmida\u003cem\u003e)\u003c/em\u003e; Chien Lee –\u003cem\u003e Lamellostreptus sp.\u003c/em\u003e (Spirostreptida); Trent –\u003cem\u003e Nearctodesmus salix\u003c/em\u003e (Polydesmida); Ratchada Yuenyongkeereemat –\u003cem\u003e Litostrophus segregatus\u003c/em\u003e (Spirobolida); Chung-Der Hsiao –\u003cem\u003e Julida sp.\u003c/em\u003e (Julida); Cricket Raspet – \u003cem\u003eBlaniulus guttulatus\u003c/em\u003e (Blaniulidae); Casey H. Richart –\u003cem\u003eLamparia bentonensis\u003c/em\u003e (Chordeumatida); Pavel Kirillov –\u003cem\u003e Zoosphaerium neptunus \u003c/em\u003e(Glomerida); H. K. Tang – \u003cem\u003eScutigeromorpha sp.\u003c/em\u003e(Scutigeromorpha), Mayah Peterson –\u003cem\u003e Hemiscolopendra marginata \u003c/em\u003e(Scolopendromorpha); Shreyas Kuchibhotla – \u003cem\u003eStenotaenia linearis \u003c/em\u003e(Geophilidae); Max J. Ford – \u003cem\u003eStrigamia sp.\u003c/em\u003e (Linotaeniidae); Felix Riegel –\u003cem\u003e Henia vesuviana \u003c/em\u003e(Dignathodontidae); Alexis Tinker-Tsavalas –\u003cem\u003e Lithobius forficatus\u003c/em\u003e (Lithobiomorpha).\u003c/p\u003e","description":"","filename":"floatimage1.png","url":"https://assets-eu.researchsquare.com/files/rs-8918891/v1/385474cb434109b33d31d0d9.png"},{"id":104401398,"identity":"e6205840-247e-47ac-a344-1514b86a062a","added_by":"auto","created_at":"2026-03-11 12:12:35","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":3728866,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eEXOGAP annotation workflow for repetitive elements.\u003c/strong\u003e This Nextflow-based workflow integrates multiple tools to provide a standardized and comprehensive annotation of REs.\u003c/p\u003e","description":"","filename":"floatimage2.png","url":"https://assets-eu.researchsquare.com/files/rs-8918891/v1/2f6a54ff99652ca88797629d.png"},{"id":103941580,"identity":"a6db6501-740b-4525-9a2e-95dd6c71879e","added_by":"auto","created_at":"2026-03-04 19:27:56","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":801049,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eGenome assembly size, load, coverage and relative proportion of REs in myriapod genomes\u003c/strong\u003e.\u003c/p\u003e","description":"","filename":"floatimage3.png","url":"https://assets-eu.researchsquare.com/files/rs-8918891/v1/ff211f9651e4263b4a59a46e.png"},{"id":103941585,"identity":"06c1e7e5-669c-4e78-91ff-7f36bd7b22c6","added_by":"auto","created_at":"2026-03-04 19:27:56","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":835368,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eTE superfamily diversity in Myriapoda genomes. \u003c/strong\u003eThe presence of TE superfamilies is represented by filled cells, with the color gradient indicating the log10-transformed number of copies.\u003cstrong\u003e \u003c/strong\u003eGrey cells denote the absence of specific TE superfamilies. TE orders are color-coded, as shown in the legend.\u003c/p\u003e","description":"","filename":"floatimage4.png","url":"https://assets-eu.researchsquare.com/files/rs-8918891/v1/8a7673ac281c0662a24f5993.png"},{"id":104402675,"identity":"71a7278e-33df-4285-bd02-cd6211fa6e7c","added_by":"auto","created_at":"2026-03-11 12:16:04","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":217645,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eRelationships between RE content and assembly size in 37 myriapod genomes. \u003c/strong\u003eThe grey area represents the 95% confidence interval.\u003cstrong\u003e A. \u003c/strong\u003eRelationships between load and assembly size in Diplopoda. \u003cstrong\u003eB.\u003c/strong\u003eRelationships between coverage and assembly size in Diplopoda. \u003cstrong\u003eC. \u003c/strong\u003eRelationships between load and assembly size in Chilopoda. \u003cstrong\u003eD.\u003c/strong\u003eRelationships between coverage and assembly size in Chilopoda.\u003c/p\u003e","description":"","filename":"floatimage5.png","url":"https://assets-eu.researchsquare.com/files/rs-8918891/v1/d0c4985b5a21c00f004664a6.png"},{"id":104401804,"identity":"1a996f36-22fe-4396-b22e-41e210d57070","added_by":"auto","created_at":"2026-03-11 12:13:35","extension":"png","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":925060,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eTransposable element landscapes. \u003c/strong\u003eThe landscapes depict the accumulation history of TEs across myriapod genomes. The x-axis represents CpG-adjusted Kimura divergence, indicating the evolutionary age of TEs, while the y-axis shows the percentage of the genome occupied by TEs (note: y-axis scales differ between plots). Different TE types are distinguished by colors as shown in the legend.\u003c/p\u003e","description":"","filename":"floatimage6.png","url":"https://assets-eu.researchsquare.com/files/rs-8918891/v1/a3ec59e931fa399a3a8f87f6.png"},{"id":103941583,"identity":"df9d7546-866d-4e0d-91a4-0c0faf869e1a","added_by":"auto","created_at":"2026-03-04 19:27:56","extension":"png","order_by":7,"title":"Figure 7","display":"","copyAsset":false,"role":"figure","size":267530,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eComparative analysis of repetitive elements detected by different studies\u003c/strong\u003e. The coverage of detected TEs with the respective proportions of TE orders (DNA transposons, LINE, LTR, SINE, and Unknown) in 9 genomes previously annotated. Results from our study are compared to those reported in the literature.\u003c/p\u003e","description":"","filename":"floatimage7.png","url":"https://assets-eu.researchsquare.com/files/rs-8918891/v1/0ca1ff8239110b88af6f7117.png"},{"id":105904709,"identity":"792070c9-5603-4823-811e-48fdc9965ea8","added_by":"auto","created_at":"2026-04-01 10:10:21","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":9319572,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8918891/v1/f239ec5d-84a1-4e88-8a4a-3c6184f0e257.pdf"},{"id":103941579,"identity":"fac8683b-99f6-4805-9616-b0101a65f0cc","added_by":"auto","created_at":"2026-03-04 19:27:56","extension":"csv","order_by":0,"title":"","display":"","copyAsset":false,"role":"supplement","size":1526,"visible":true,"origin":"","legend":"","description":"","filename":"supplementarytable1.csv","url":"https://assets-eu.researchsquare.com/files/rs-8918891/v1/efef13d2010fa04f597bb131.csv"},{"id":104401541,"identity":"32f61dc9-a7af-4ef9-bbb5-b7044c3fec61","added_by":"auto","created_at":"2026-03-11 12:12:57","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":161959,"visible":true,"origin":"","legend":"","description":"","filename":"supplementaryfigure4.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8918891/v1/6a3da922dc7485db8513d88a.pdf"},{"id":104401670,"identity":"c2ee8b24-cdb7-4da0-8e31-ff5d9f07c46e","added_by":"auto","created_at":"2026-03-11 12:13:14","extension":"pdf","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":239176,"visible":true,"origin":"","legend":"","description":"","filename":"supplementaryfigure1.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8918891/v1/0b0474301ef6a98d8d58cfff.pdf"},{"id":103941589,"identity":"d7f1d823-5a76-4856-bfef-814fa71b24bb","added_by":"auto","created_at":"2026-03-04 19:27:56","extension":"pdf","order_by":3,"title":"","display":"","copyAsset":false,"role":"supplement","size":439883,"visible":true,"origin":"","legend":"","description":"","filename":"supplementaryfigure3.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8918891/v1/72f772ccd326a2c543ca0860.pdf"},{"id":104401615,"identity":"bd13f100-dd7d-4f1a-9e53-2d0817bdae08","added_by":"auto","created_at":"2026-03-11 12:13:09","extension":"pdf","order_by":4,"title":"","display":"","copyAsset":false,"role":"supplement","size":437555,"visible":true,"origin":"","legend":"","description":"","filename":"supplementaryfigure2.pdf","url":"https://assets-eu.researchsquare.com/files/rs-8918891/v1/3beda0af1317f7f0eb58ea3a.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Repetitive Elements in Myriapoda: Genomic Diversity and Evolution","fulltext":[{"header":"Background","content":"\u003cp\u003eMyriapoda are a fascinating and relatively understudied group within the arthropod phylum, characterized by their segmented bodies and numerous legs. They play critical roles in soil and forest ecosystems, contributing significantly to soil aeration, decomposition, and nutrient and water cycling [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e, \u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e]. This diverse group comprises four classes: Chilopoda (centipedes), Diplopoda (millipedes), Pauropoda, and Symphyla (garden centipedes or pseudocentipedes).\u003c/p\u003e \u003cp\u003eThe Diplopoda class is the most diverse, with around 13,000 known species across 16 orders [\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e, \u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e]. Millipedes are characterized by having two pairs of legs on most trunk segments, and although the name \u0026ldquo;millipede\u0026rdquo; suggests a thousand legs, most species have far fewer. However, the recently described species \u003cem\u003eEumillipes persephone\u003c/em\u003e reaches a record 330 segments and up to 1,306 legs, the highest number known in any animal [\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e]. They primarily feed on decaying plant matter, making them important decomposers that enhance soil quality and nutrient cycling [\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e, \u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e]. Chilopods have one pair of legs per segment and are characterized by rapid movement. They range from 14 to 177 pairs of legs [\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e] and possess venomous forcipules, specialized claws used for predation [\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e]. This class includes over 3,000 known species divided into five orders [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e] and is unique among myriapods for its carnivorous diet. The lesser-known classes, Pauropoda and Symphyla, are smaller and feature simpler segmentation patterns with fewer legs. Pauropoda have 12 partially fused segments with 8 to 11 pairs of legs, including a reduced first pair [\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e], and consist of about 990 known species in two orders [\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e]. They feed on fungus hyphae, spores, and plant tissue [\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e]. Symphyla, with 15 to 22 body segments but only 11 or 12 pairs of legs, contains roughly 200 known species in a single order [\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e]. They mainly feed saprophagous, but some species are also predators. These classes, although less diverse and less well studied, contribute to diverse ecological functions within their habitats.\u003c/p\u003e \u003cp\u003eThe diverse morphologies and ecological functions of myriapods underscore their ecological significance across various environments. Despite their importance, the exploration of myriapod genetics and genomics has historically lagged behind that of other arthropod groups, such as insects and crustaceans. However, recent advances in sequencing technologies have begun to bridge this gap. The first myriapod genome, that of \u003cem\u003eStrigamia maritima\u003c/em\u003e, was sequenced in 2011 [\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e]. This was followed by the sequencing of the first diplopod genomes, \u003cem\u003eHelicorthomorpha holstii\u003c/em\u003e and \u003cem\u003eTrigoniulus corallinus\u003c/em\u003e [\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e]. An additional seven genomes of varying quality were provided by a 2020 study on myriapod genomics [\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]. A major breakthrough in myriapod genomics came with the MetaInvert project, an international initiative that gathered genomic data from 232 invertebrate species, including 45 myriapods [\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]. At the time of writing, the number of available myriapod genomes has increased to 68.\u003c/p\u003e \u003cp\u003eIn terms of genome size, most available myriapod assemblies range from 118.1 Mb to 800 Mb. Hovewer, seven species have genomes larger than 1 Gb, and four of them exceed 2 Gb: \u003cem\u003eAgaricogonopus acrotrifoliolatus\u003c/em\u003e (2.2 Gb), \u003cem\u003eThereuonema tuberculata\u003c/em\u003e (2.4 Gb), \u003cem\u003eRhysida immarginata\u003c/em\u003e (2.5 Gb) and \u003cem\u003eLithobius niger\u003c/em\u003e (3.2 Gb) [\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]. This marked variation suggests substantial differences in genome architecture, yet the underlying drivers\u0026mdash;such as repetitive element accumulation\u0026mdash;remain poorly characterized. The quality of genome assemblies varies considerably, with only 7 genomes assembled at the chromosomal level, while the others remain at the scaffold or contig level. The genomes of symphylans and pauropods are among the most fragmented. So, comprehensive genomic resources for myriapods remain scarce, and much of their genome architecture, including repetitive elements, remains largely unexplored.\u003c/p\u003e \u003cp\u003eRepetitive elements (REs), long considered as non-functional \"junk\" DNA, are now recognized for their critical roles in genome organization, regulation, and evolution [\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e]. Beyond their significant influence on genome size, REs also shape the structure and drive the evolution of eukaryotic genomes. However, their repetitive nature poses substantial challenges for genome assembly and annotation [\u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e], complicating their accurate identification and classification, and the understanding of their impact on host genomes. REs can be broadly categorized into two main types: transposable elements (TEs) and tandem repeats (TRs), each with distinct characteristics and biological functions.\u003c/p\u003e \u003cp\u003eTEs, often referred to as \"jumping genes,\" are DNA sequences capable of moving from one location to another within the genome, significantly impacting genomic stability and gene function. For example, they contribute to the regulation of gene expression by recruiting silencing machinery [\u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e], which represses gene expression via epigenetic modifications. Additionally, TEs contribute to genome evolution by serving as origin of some microRNAs [\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e]. They are classified into two primary groups based on their transposition intermediate: RNA-mediated elements (class I, or retrotransposons) and DNA-mediated elements (class II, or DNA transposons) [\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e, \u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eClass I TEs use a mechanism commonly called \u0026ldquo;copy and paste\u0026rdquo;. This process starts with the transcription of the DNA sequence into RNA, which is then reverse transcribed into DNA by a TE-encoded reverse transcriptase (RT) and inserted into a new genomic location [\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e]. They include Long Terminal Repeat (LTR), Non-LTR retrotransposons, DIRS-like elements, and Penelope-like elements (PLEs). LTR retrotransposons are defined by the presence of long repeated sequences at both ends. They resemble retroviruses and span from a few hundred to several thousand base pairs. Non-LTR retrotransposons distinguished by the absence of LTRs are organized into 2 orders: Long Interspersed Nuclear Elements (LINEs) and Short Interspersed Nuclear Elements (SINEs). Both LINEs and SINES possess a poly-A tail at the 3' end and are flanked by target site duplications. LINEs are autonomous retrotransposons that encode reverse transcriptase and are typically over 5 kb in length. In animal genomes, LINEs are abundant; for instance, 100 LINE subfamilies alone constitute approximately 3% of the malaria mosquito \u003cem\u003eAnopheles gambiae\u003c/em\u003e genome [\u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e24\u003c/span\u003e]. SINEs are short (\u0026lt;\u0026thinsp;700 bp) non-autonomous retrotransposons that rely on LINE-encoded reverse transcriptase for their reverse transcription. SINEs play a role in genetic variation, providing regulatory elements for gene expression or alternative splice sites [\u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e25\u003c/span\u003e]. DIRS-like elements are a divergent group of retroelements that encode RT but differ by containing a Tyrosine recombinase (YR) gene instead of an integrase. The last group of retrotransposons, PLEs, have a single ORF that encodes a protein with both RT and endonuclease (EN) activities. The RT domain of PLEs is more similar to telomerase, than the RT from LTRs or LINEs. PLEs are absent from the genomes of mammals, birds, and \u003cem\u003eCaenorhabditis elegans\u003c/em\u003e, though this absence may be due to a loss event [\u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e]. The only active representative, Penelope, has been identified in \u003cem\u003eDrosophila virilis\u003c/em\u003e, and its invasion appears to be relatively recent [\u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e]. Due to their replication mechanism, which generates a new copy with each cycle, class I elements are the primary contributors to the repetitive fraction in large genomes [\u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eClass II TEs move directly from one DNA location to another without involving an RNA intermediate. Depending on the number of DNA strands cleaved during transposition, they can be further classified into two subclasses: Terminal Inverted Repeat (TIR) and Cryptons belong to subclass I, while Mavericks (or Polintons) and Helitrons belong to subclass II. TIR are characterized by inverted repeat sequences at their ends and encode the transposase that binds near the inverted repeat to mediate mobility [\u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e]. Cryptons, however, lack transposase and instead rely on a tyrosine recombinase for their movement. Initially identified in fungi, they have since been shown to be present in a broader range of species, including insects [\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e]. Helitrons and Mavericks use a rolling-circle mechanism to move and can capture and mobilize fragments of other genomic regions, thereby contributing to genetic diversity and genomic rearrangements [\u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e29\u003c/span\u003e]. Helitrons are found in plants, fungi and mammals [\u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e], while Mavericks are large transposons commonly found in eukaryotic genomes, except for plants [\u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eIn addition to TEs, TRs represent another important aspect of genomic organization. These are DNA sequences in which units are repeated adjacently in a head-to-tail arrangement. They are categorized into several orders, including microsatellites, minisatellites, and satellites. Microsatellites, also known as Simple Sequence Repeats, are highly variable among individuals and populations, making them valuable for genetic mapping and population genetics studies. Additionally, microsatellites can influence gene function and contribute to genetic diversity. In contrast, minisatellites are longer and are often found in telomeric regions of the genome. They are associated with genomic instability and chromosomal rearrangements and can affect gene regulation and epigenetic modifications [\u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e32\u003c/span\u003e]. Satellites, the third class, are composed of even larger repeating units, ranging from a few hundred to several thousand base pairs. Satellites are typically located in centromeric and pericentromeric regions of chromosomes, where they play crucial roles in chromosome structure and segregation during cell division. Due to their repetitive nature and size, satellite DNA is often involved in maintaining chromosomal stability and can contribute to evolutionary changes in genome structure.\u003c/p\u003e \u003cp\u003eConsidering their significant roles, REs have been extensively studied in Arthropoda, particularly in insects [\u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e] where their abundance greatly varies among orders and even between species belonging to the same order. In Diptera for example, the TE content ranges from less than 1% in \u003cem\u003eBelgica antarctica\u003c/em\u003e to around 55% in the yellow fever mosquito \u003cem\u003eAedes aegypti\u003c/em\u003e. Even among closely related \u003cem\u003eDrosophila\u003c/em\u003e species, the TE content ranges from 10% (in \u003cem\u003eD. miranda\u003c/em\u003e and \u003cem\u003eD. simulans\u003c/em\u003e) to 40% (in \u003cem\u003eD. ananassae\u003c/em\u003e). The highest TE content (60%) was found in the large genome (6.5 Gb) of the migratory locust \u003cem\u003eLocusta migratoria\u003c/em\u003e (Orthoptera). While most REs have been characterized in well-studied model species such as \u003cem\u003eD. melanogaster\u003c/em\u003e, classification of REs is often difficult in non-model species. For example, unknown elements account for up to 93% of TEs in the mayfly \u003cem\u003eEphemera danica\u003c/em\u003e. Unlike insects, very little is known about the REs of myriapods. The first comparative study between three species [\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e] highlights the importance of LINEs and DNA transposons in the expansion of the \u003cem\u003eT. corallinus\u003c/em\u003e genome, with TE coverage reaching 55%, whereas TEs represent only 19% of the \u003cem\u003eH. holstii\u003c/em\u003e genome. This substantial variability seems to indicate that TEs are major players in the dynamics of Myriapod genomes.\u003c/p\u003e \u003cp\u003eThe aim of our study is to provide a comprehensive analysis of REs across a large range of myriapod species based on a standardized RE annotation protocol. Our annotation of REs in 37 genomes allowed us to characterize the diversity and respective abundance of the different families making up the myriapod repeatome. By comparing TE composition across species, we identified common patterns as well as lineage-specific variations, highlighting both conserved and divergent evolutionary trajectories. Furthermore, we examined the relationship between RE content and genome assembly size, revealing contrasting trends between Diplopoda and Chilopoda. Finally, through an analysis of TE landscapes and divergence patterns, we explored the evolutionary dynamics of REs in Myriapoda, shedding light on their role in genome plasticity and lineage diversification.\u003c/p\u003e"},{"header":"Materials and methods","content":"\u003cdiv id=\"Sec3\" class=\"Section2\"\u003e \u003ch2\u003eGenomic datasets\u003c/h2\u003e \u003cp\u003eThe myriapod genome assemblies were retrieved from the NCBI Genome database [\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e] in August 2025. Genomes were selected based on data quality by requiring a BUSCO (version 6.0.0) [\u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e] completeness score above 70%, assessed using the Arthropoda OrthoDB v10 dataset [\u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e36\u003c/span\u003e], and a contig N50 greater than 5 kb (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). Additionally, only one genome per species was retained based on the quality of the assembly, except for \u003cem\u003eStrigamia acuminata\u003c/em\u003e. For this species, two genomes were included for comparison purposes: one provided by the Darwin Tree of Life project [\u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e, \u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e], assembled at the chromosomal level, and another by MetaInvert, assembled at the contig level. This selection process yielded a final dataset comprising 36 species (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003e) and 37 genomes, including 16 Chilopoda and 20 Diplopoda species. Unfortunately, no genomes from Symphyla or Pauropoda met the quality criteria for inclusion in the analysis.\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab1\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003e\u003cb\u003eGenomic datasets used in this study.\u003c/b\u003e For \u003cem\u003eStrigamia acuminata\u003c/em\u003e, two assemblies were retained: one assembled at the chromosomal level (chrom.) and the other at the contig level (cont.).\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"8\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c3\" colnum=\"3\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c4\" colnum=\"4\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c5\" colnum=\"5\"\u003e\u003c/div\u003e \u003cdiv align=\"char\" char=\".\" class=\"colspec\" colname=\"c6\" colnum=\"6\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c7\" colnum=\"7\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c8\" colnum=\"8\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eClass\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eOrganism Name\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c3\"\u003e \u003cp\u003eAssembly Accession\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c4\"\u003e \u003cp\u003eAssembly level\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c5\"\u003e \u003cp\u003eAssembly size (Mb)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c6\"\u003e \u003cp\u003eContig N50\u003c/p\u003e \u003cp\u003e(kb)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c7\"\u003e \u003cp\u003eBUSCO\u003c/p\u003e \u003cp\u003e-C (%)\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c8\"\u003e \u003cp\u003eRef.\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"16\" rowspan=\"17\"\u003e \u003cp\u003eChilopoda\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eCryptops parisi\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_034695005.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eContig\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e304\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e14.7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e77.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eGeophilus carpophagus\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_034687075.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eContig\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e141\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e8.0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e82.7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eGeophilus flavus\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_034695885.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eContig\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e187\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e5.7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e72.7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eGeophilus truncorum\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_034695745.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eContig\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e137\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e12.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e83.4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eHenia vesuviana\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_034696185.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eContig\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e148\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e5.4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e80.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eLithobius niger\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_023313725.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eScaffold\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e3,238\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e15.4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e70.4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eLithobius variegatus\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_965125955.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eChromosome\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e1,767\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e2,691.4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e98.6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e39\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003ePachymerium ferrugineum\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_034686365.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eContig\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e118\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e28.3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e81.7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eRhysida immarginata\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_023313115.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eScaffold\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e2,529\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e33.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e89.9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eScolopendra cretica\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_966189295.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eChromosome\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e1,456\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e81,956.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e97.7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eStenotaenia linearis\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_034700445.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eScaffold\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e148\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e8.0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e77.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eStrigamia acuminata (chrom.)\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_949358305.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eChromosome\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e238\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e1,816.0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e98.9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eStrigamia acuminata (cont.)\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_034703045.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eContig\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e131\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e11.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e77.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eStrigamia crassipes\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_034683725.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eContig\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e131\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e14.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e77.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eStrigamia maritima\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_000239455.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eScaffold\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e176\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e24.7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e98\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eStrigamia transsilvanica*\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_034701245.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eScaffold\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e124\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e12.4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e71.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eThereuonema tuberculata\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_023159025.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eScaffold\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e2,458\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e23.0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e91.6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\" morerows=\"19\" rowspan=\"20\"\u003e \u003cp\u003eDiplopoda\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eAgaricogonopus acrotrifoliolatus\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_052040765.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eChromosome\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e2,241\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e360,240.6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e98.4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eBrachycybe producta\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_036925085.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eScaffold\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e295\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e1,616.7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e98.3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e\u0026nbsp;\u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eChoneiulus palmatus\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_965278725.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eChromosome\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e627\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e1,186.7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e98.4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eCylindroiulus punctatus\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_034695085.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eChromosome\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e354\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e1,367.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e98.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e41\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eGlomeris maerens\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_023279145.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eScaffold\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e150\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e9.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e85.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eGlomeris marginata\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_034696005.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eContig\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e163\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e9.0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e71.7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eHelicorthomorpha holstii\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_013389785.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eScaffold\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e181\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e59.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e96.7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eJulidae sp. JJ-2019**\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_023279205.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eScaffold\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e613\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e15.4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e89.9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eJulus scandinavius\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_034696685.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eContig\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e251\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e9.9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e72.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eJulus scanicus\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_034698625.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eContig\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e251\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e12.2\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e74.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eKryphioiulus occultus\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_034687865.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eContig\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e229\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e18.3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e72.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eMegaphyllum sjaelandicum\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_034698745.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eContig\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e333\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e9.9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e73.7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eNanogona polydesmoides\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_965153395.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eChromosome\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e406\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e781.0\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e98\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e42\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eOmmatoiulus sabulosus\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_034697705.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eContig\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e334\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e9.5\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e73.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003ePlatydesmidae sp. JHPL-2020**\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_023159045.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eScaffold\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e328\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e8.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e91.7\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003ePolydesmus complanatus\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_034692225.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eContig\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e164\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e29.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e82.6\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eProteroiulus fuscus\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_034700285.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eContig\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e259\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e7.4\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e73.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eRossiulus vilnensis\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_034700785.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eContig\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e211\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e19.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e73.9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eTrigoniulus corallinus\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_013389805.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eScaffold\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e449\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e54.3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e97.8\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eXestoiulus laeticollis\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c3\"\u003e \u003cp\u003eGCA_034698905.1\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c4\"\u003e \u003cp\u003eContig\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c5\"\u003e \u003cp\u003e304\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"char\" char=\".\" colname=\"c6\"\u003e \u003cp\u003e10.3\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c7\"\u003e \u003cp\u003e76.9\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c8\"\u003e \u003cp\u003e[\u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e]\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e \u003cp\u003e*: the genome was originally published under the species name of \u003cem\u003eS. transsilvanica\u003c/em\u003e, but following taxonomic revision, it has been reassigned to \u003cem\u003eS. crassipes\u003c/em\u003e.\u003c/p\u003e \u003cp\u003e**: \u003cem\u003eP. sp. JHPL-2020\u003c/em\u003e et \u003cem\u003eJ. sp. JJ-2019\u003c/em\u003e are respectively referenced as \u003cem\u003eNiponia nodulosa\u003c/em\u003e and \u003cem\u003eAnaulaciulus tonginus\u003c/em\u003e in So et al. article [\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e].\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003c/div\u003e\n\u003ch3\u003eAnnotation of repetitive elements\u003c/h3\u003e\n\u003cdiv id=\"Sec5\" class=\"Section2\"\u003e \u003ch2\u003eIdentification of TEs\u003c/h2\u003e \u003cp\u003e \u003cem\u003eDe novo\u003c/em\u003e identification of REs was initially performed using RepeatModeler2 (version 2.0.3, with the options \u003cem\u003e-LTRStruct and -engine ncbi\u003c/em\u003e) [\u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e43\u003c/span\u003e] (Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003e). This software leverages tools such as LTRharvest (version 1.6.4) [\u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e44\u003c/span\u003e] and LTR_retriever (version 2.9.4) [\u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e45\u003c/span\u003e] to enhance the detection of LTR.\u003c/p\u003e \u003cp\u003eAll consensus families generated by RepeatModeler2 were then provided to MCHelper [\u003cspan citationid=\"CR46\" class=\"CitationRef\"\u003e46\u003c/span\u003e] (version 1.7.1 fully automated mode with -b arthropoda_odb10.hmm) for curation and refinement. MCHelper removes false positives such as consensus sequences corresponding to multicopy protein-coding genes or short TRs, extends incomplete consensus sequences using the BEE (Blast\u0026ndash;Extract\u0026ndash;Extend) algorithm, identifies conserved TE domains and characteristic structural features, and classifies previously uncharacterized consensus sequences using a combination of homology search, domain inference, and structural evaluation.\u003c/p\u003e \u003cp\u003eFinally, libraries from all species were combined and clustered with the arthropoda section of the RepBase library (version 26.05, May 2021; 19,232 sequences in this section) [\u003cspan citationid=\"CR47\" class=\"CitationRef\"\u003e47\u003c/span\u003e] using CD-HIT-EST (version 4.7, options \u003cem\u003e-c 0.95 -g 1 -n 10 -l 80 -aS 98\u003c/em\u003e).\u003c/p\u003e \u003cp\u003eThis process resulted in a final TE library, which was subsequently used for annotation of REs with RepeatMasker (version 4.1.2-p1) using the options \u003cem\u003e-e ncbi -a -gccalc -norna -excln -s\u003c/em\u003e. TRs were annotated using RepBase and Tandem Repeat Finder (TRF) [\u003cspan citationid=\"CR48\" class=\"CitationRef\"\u003e48\u003c/span\u003e] integrated in RepeatMasker.\u003c/p\u003e \u003cp\u003eThe procedures described above are included in the module dedicated to REs of EXOGAP (EXotic Organism Genome Annotation Pipeline), a Nextflow pipeline (version 24.04.1) available on GitHub (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://github.com/dorinemerlat/exogap\u003c/span\u003e\u003cspan address=\"https://github.com/dorinemerlat/exogap\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003cspan type=\"Underline\" class=\"Underline\" name=\"Emphasis\"\u003e).\u003c/span\u003e\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003c/div\u003e\n\u003ch3\u003eCorrelation between genome size and TE abundance\u003c/h3\u003e\n\u003cp\u003eTo estimate the contribution of REs to myriapod genomes, we calculated TE coverage as the proportion of the genome occupied by TEs. Prior to coverage calculation, RepeatMasker annotations were filtered to exclude low-complexity sequences, and overlapping TE annotations were merged using \u003cem\u003ebedtools merge\u003c/em\u003e [\u003cspan citationid=\"CR49\" class=\"CitationRef\"\u003e49\u003c/span\u003e] (version v2.31.1) to avoid biased estimates caused by overlapping intervals. TE load was defined as the total number of TE copies per genome. Relationships between TE load or TE coverage and genome assembly size or assembly contiguity (measured by N50) were assessed using both linear regression and Spearman rank correlation analyses. Statistical significance was considered at p\u0026thinsp;\u0026lt;\u0026thinsp;0.05. These analyses were performed in R [\u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e50\u003c/span\u003e] using the \u003cem\u003elm\u003c/em\u003e function and the \u003cem\u003eggplot2\u003c/em\u003e package [\u003cspan citationid=\"CR51\" class=\"CitationRef\"\u003e51\u003c/span\u003e] for data visualization. Additionally, we generated a heatmap using ggplot2 to compare TE composition across species.\u003c/p\u003e\n\u003ch3\u003eHeatmap visualization of TE composition\u003c/h3\u003e\n\u003cp\u003eHeatmaps comparing TE composition across species were generated in R using the package \u003cem\u003eComplexHeatmap\u003c/em\u003e (version 2.26.1) [\u003cspan citationid=\"CR52\" class=\"CitationRef\"\u003e52\u003c/span\u003e]. TE load and TE coverage values were log-transformed prior to visualization to enable comparison among species with large differences in repeat abundance. TE annotations classified as unknown were excluded from the heatmaps.\u003c/p\u003e \u003cdiv id=\"Sec8\" class=\"Section2\"\u003e \u003ch2\u003eEstimating TE age distribution using kimura distance\u003c/h2\u003e \u003cp\u003eTo infer the relative age distribution of REs, we estimated sequence divergence using Kimura two-parameter distances, which consider differences in transition and transversion rates. These calculations were performed using the RepeatMasker helper scripts \u003cem\u003ecalcDivergenceFromAlign.pl\u003c/em\u003e and \u003cem\u003ecreateRepeatLandscape.pl\u003c/em\u003e. The Kimura distance was computed between each TE copy and its respective consensus sequence, allowing us to infer TE age distributions across species. A peak at low Kimura distances indicates recent TE activity, whereas higher divergence values reflect older TE insertions subjected to genetic drift or mutation accumulation. TE landscapes were generated for each species to compare the dynamics of TE expansions using \u003cem\u003eggplot2\u003c/em\u003e.\u003c/p\u003e \u003c/div\u003e"},{"header":"Results","content":"\u003cdiv id=\"Sec10\" class=\"Section2\"\u003e \u003ch2\u003eOverview of the Myriapoda repeatome\u003c/h2\u003e \u003cp\u003eWe conducted a standardized analysis of 37 Myriapoda genomes from 36 species. Using RepeatModeler2 and MCHelper, we identified \u003cem\u003ede novo\u003c/em\u003e a total of 54,785 RE families with 54,8% successfully assigned to known RE families.\u003c/p\u003e \u003cp\u003eTRs are present in all myriapod species (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e), though their proportions vary. In terms of total copy number, the centipedes \u003cem\u003eT. tuberculata and Scolopendra cretica\u003c/em\u003e, contain the highest TR loads, with approximately 798,000 and 434,000 copies, respectively. However, when considering genome coverage, the highest proportions are found in the millipedes \u003cem\u003eBrachycybe producta\u003c/em\u003e (3.44% TR coverage) and \u003cem\u003eP. Complanatus (2.28%)\u003c/em\u003e.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eThe analysis of TEs across Myriapoda species reveals substantial variations in TE abundance and composition (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e). TE coverage (defined as the proportion of the genome occupied by TEs) ranges from 16% in \u003cem\u003ePolydesmus complanatus\u003c/em\u003e to 81% in \u003cem\u003eA. acrotrifoliolatus\u003c/em\u003e, although \u003cem\u003eP. complanatus\u003c/em\u003e is not the smallest genome analyzed. The number of TE copies (load) varies dramatically, from 0.14\u0026nbsp;million in \u003cem\u003ePachymerium ferrugineum\u003c/em\u003e to 8.78\u0026nbsp;million in \u003cem\u003eL. niger\u003c/em\u003e, which is also the species with the largest genome among the species studied.\u003c/p\u003e \u003cp\u003eAcross all Myriapoda, TIR elements dominate in most genomes in terms of both load and coverage. LTR elements typically rank second in coverage across these genomes, while the importance of LINEs varies considerably between species. Within the Diplopoda class, the Julida order exhibits consistent TE coverage and load across species, with a notable abundance of TIR elements. In the other diplopod genomes, the composition and importance of the repeatome is more diverse with certain species having unique TE patterns compared with all the myriapod genomes studied. \u003cem\u003eT. corallinus\u003c/em\u003e is the only species with a significant proportion of SINE elements (9% of TE coverage), far exceeding the next highest value of 2% in \u003cem\u003eChoneiulus palmatus\u003c/em\u003e. Additionally, \u003cem\u003eA. acrotrifoliolatus\u003c/em\u003e has the highest proportion of LINE elements (29.6% of TE coverage), followed by \u003cem\u003eT. corallinus\u003c/em\u003e (28.1%), \u003cem\u003eJulidae. sp. JJ 2019\u003c/em\u003e (14%) and \u003cem\u003eR. immarginata\u003c/em\u003e (13.6%). The Chilopoda class also exhibits substantial variability in TE composition. LINEs are present at low abundance in Geophilomorpha genomes, accounting for no more than 0.84% of TE coverage. This pattern suggests a possible loss of most LINE elements in Geophilomorpha. In some chilopods, including the two Lithobiomorpha genomes and \u003cem\u003eR. immarginata\u003c/em\u003e, Maverick elements contribute substantially to the TE load, with ~\u0026thinsp;89,000 copies in \u003cem\u003eL. niger\u003c/em\u003e, ~\u0026thinsp;39,000 copies in Lithobius \u003cem\u003evariegatus\u003c/em\u003e, and ~\u0026thinsp;38,000 copies in \u003cem\u003eR. immarginata\u003c/em\u003e.\u003c/p\u003e \u003cp\u003eSurprisingly, LTR elements occur in highly variable proportions across both diplopods and chilopods. In several species, they represent a substantial fraction of TE composition, notably in Cylindroiulus \u003cem\u003epunctatus\u003c/em\u003e and \u003cem\u003eS. maritima\u003c/em\u003e, where LTR elements account for 54.2% and 52.5% of the composition of the TE coverage, respectively. However, in most analyzed genomes, LTR elements constitute a much smaller fraction, typically representing less than 30% of the composition of the TE coverage, indicating that they are not the dominant TE order across Myriapoda. No clear association between LTR abundance and myriapod classes was detected, as high and low LTR proportions occur in both diplopods and chilopods.\u003c/p\u003e \u003cp\u003eComparison of the two available \u003cem\u003eS. acuminata\u003c/em\u003e assemblies further illustrates the impact of assembly contiguity on LTR detection. The chromosome-level assembly shows substantially higher TE coverage than the contig-level assembly (58.3% versus 36.4%) and, to a lesser extent, a higher TE copy number (462,000 versus 351,000 copies). This difference is largely driven by increased recovery of LTR elements, whose genomic coverage rises from 7.5% to 28.0%. These results indicate that fragmented assemblies may substantially underestimate the contribution of long and nested elements such as LTR retrotransposons.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec11\" class=\"Section2\"\u003e \u003ch2\u003eTE composition\u003c/h2\u003e \u003cp\u003eThe analysis of the repeatome composition in myriapod genomes reveals a remarkable diversity (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e for the load and \u003cb\u003eSupplementary Fig.\u0026nbsp;1\u003c/b\u003e for the coverage), with almost all known TE superfamilies represented in at least one species. Only a small number of TE groups\u0026mdash;including Casposons, Novosib, IR4, and SINE families lacking a canonical RNA polymerase III promoter or associated with tRNA and 5S RNA\u0026mdash;remain undetected across all analyzed genomes, suggesting either true absence or extremely low abundance in Myriapoda. Several species exhibit globally darker vertical patterns in the heatmaps, indicating elevated TE representation across multiple TE groups. These patterns largely correspond to species with the largest genome assemblies, suggesting genome-wide TE accumulation rather than expansions restricted to particular TE families.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eAt the superfamily and family levels, TE profiles reveal a shared backbone of repetitive elements across both Diplopoda and Chilopoda, suggesting the presence of a conserved ancestral TE repertoire in myriapods with lineage-specific quantitative variations. Despite substantial variation in genome size and TE composition among species, several TE groups remain consistently abundant across most analyzed genomes. Among class II elements, terminal inverted repeat (TIR) DNA transposons represent the most prevalent groups, particularly the CACTA, Mutator, hAT, PIF/Harbinger, and Tc1/Mariner superfamilies. Rolling-circle Helitrons and large DNA elements such as Mavericks are also widely distributed, although their abundance varies markedly among species. Overall, Helitrons and Mavericks are recurrent components of myriapod genomes, albeit generally contributing less than the dominant TIR elements. Among class I elements, LTR retrotransposons constitute a major component of TE repertoires in many species, with Gypsy elements being particularly abundant, alongside Copia, Bel-Pao, and several unclassified LTR groups. LINE elements, especially RTE and CR1/Jockey-related clades, are likewise widespread across taxa, although their relative genomic contributions differ substantially among lineages, indicating lineage-specific histories of expansion and retention.\u003c/p\u003e \u003cp\u003eBeyond these highly represented superfamilies, clear compositional differences are observed between Diplopoda and Chilopoda, as well as within these groups. Within Diplopoda, and particularly among Julida, many TE families and superfamilies show comparable coverage patterns across species, and generally display TE repertoires dominated by DNA transposons, particularly TIR elements. This is consistent with shared evolutionary history and broadly similar TE dynamics within this clade. \u003cem\u003eT. corallinus\u003c/em\u003e stands out with a high abundance of LINEs I R1 and RTE, and 5S \u0026ndash; Deu-core rRNA-derived. Additional differences at the TE family level are presented in \u003cb\u003eSupplementary Fig.\u0026nbsp;2\u003c/b\u003e (load) and \u003cb\u003eSupplementary Fig.\u0026nbsp;3\u003c/b\u003e (coverage). Among Chilopoda, a common TE background is likewise evident, with LINEs, LTRs, and DNA transposons consistently present across all species. However, contrasts among the major clades are more pronounced than within Diplopoda, with notable differences observed between Scolopendromorpha, Geophilomorpha, and Scutigeromorpha.\u003c/p\u003e \u003cp\u003eAlthough MITEs appear to be detected in only two genomes, MITE elements were in fact identified by MCHelper in all analyzed genomes. Under the Dfam classification scheme used here, these short non-autonomous elements are generally assigned to their parental TIR superfamilies rather than to a dedicated MITE category, which likely explains their apparent absence from most genomes in the compositional heatmap. Actually, MITE-related insertions range from a few thousand copies in many diplopods and Geophilomorpha centipedes (typically\u0026thinsp;~\u0026thinsp;2,000\u0026ndash;30,000 copies per genome) to markedly higher values in several lineages. Particularly high numbers are observed in Lithobiomorpha (\u003cem\u003eL. niger\u003c/em\u003e, ~\u0026thinsp;165,000 copies; \u003cem\u003eL. variegatus\u003c/em\u003e, ~\u0026thinsp;96,000 copies), as well as in large chilopod genomes such as \u003cem\u003eR. immarginata\u003c/em\u003e (~\u0026thinsp;474,000 copies), \u003cem\u003eT. tuberculata\u003c/em\u003e (~\u0026thinsp;256,000 copies), and \u003cem\u003eS. cretica\u003c/em\u003e (~\u0026thinsp;120,000 copies). Elevated counts are also observed in some diplopods, including \u003cem\u003eA. acrotrifoliolatus\u003c/em\u003e (~\u0026thinsp;114,000 copies), \u003cem\u003eT. corallinus\u003c/em\u003e (~\u0026thinsp;64,000 copies), and Platydesmidae sp. JHPL 2020 (~\u0026thinsp;84,000 copies). These patterns indicate that MITE amplification varies strongly among lineages and tends to be associated with genomes already enriched in DNA transposons, suggesting that MITE dynamics broadly follow those of their autonomous TIR partners rather than forming independent expansion patterns.\u003c/p\u003e \u003cp\u003eThe load of TE superfamilies detected in the chromosome-level versus the contig-level assembly of \u003cem\u003eS. acuminata\u003c/em\u003e are comparable, except for the TIR PiggyBac elements and Maverick TEs. However, some families such as Gypsy Micropia (LTR) are found only in the chromosome-level assembly, while RTE ORTE LINEs elements are detected exclusively in the contig-level genome. This element has been identified in only a few genomes across both Chilopoda and Diplopoda, indicating it may be difficult to detect accurately.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec12\" class=\"Section2\"\u003e \u003ch2\u003eContribution of TEs to myriapod genome size\u003c/h2\u003e \u003cp\u003eA clear distinction emerges in TE load between genomes smaller than 1 Gb and larger genomes (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003e). While smaller genomes contain fewer than ~\u0026thinsp;627,000 TE copies, larger genomes harbor several million copies, ranging from ~\u0026thinsp;3.2\u0026nbsp;million in \u003cem\u003eS. cretica\u003c/em\u003e to ~\u0026thinsp;8.8\u0026nbsp;million in \u003cem\u003eL. niger.\u003c/em\u003e\u003c/p\u003e \u003cp\u003eTo investigate the contribution of TEs to genome size, we tested for correlations between TE load, TE coverage and genome assembly size in Diplopoda and Chilopoda. In Diplopoda, we observed strong positive correlations between genome assembly size and both TE load (Spearman\u0026rsquo;s rank correlation, ρ\u0026thinsp;=\u0026thinsp;0.91, p\u0026thinsp;=\u0026thinsp;0) (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003eA) and TE coverage (Spearman\u0026rsquo;s rank correlation, ρ\u0026thinsp;=\u0026thinsp;0.91, p\u0026thinsp;=\u0026thinsp;0) (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003eB). These results suggest that TEs contribute significantly to genome size variation in this group. In contrast to Diplopoda, the relationship between TE content and genome size in Chilopoda is more complex. TE load shows a strong positive correlation with genome assembly size (Spearman\u0026rsquo;s rank correlation, ρ\u0026thinsp;=\u0026thinsp;0.88, p\u0026thinsp;\u0026lt;\u0026thinsp;0.001) (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003eC), whereas TE coverage is only moderately correlated (Spearman\u0026rsquo;s rank correlation, ρ\u0026thinsp;=\u0026thinsp;0.77, p\u0026thinsp;\u0026lt;\u0026thinsp;0.001) (Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003eD), suggesting that TE coverage alone does not explain genome size variation in chilopods. In fact, the 11 Geophilimorpha assemblies, all smaller than 250 Mb, exhibit TE coverage ranging from 16.1 to 58.4%. Some of these small genomes exhibit TE coverage comparable to, or even exceeding, that of genomes larger than 1 Gb. For example, the chromosome-level assembly of \u003cem\u003eS. acuminata\u003c/em\u003e (238 Mb) achieves a TE coverage of 58.4%, which is comparable to the 60.2% coverage of the chromosome-level assembly of \u003cem\u003eL. variegatus\u003c/em\u003e and higher than the 48.7% coverage of \u003cem\u003eT. tuberculata\u003c/em\u003e, which nevertheless have much larger genomes (1.767 and 2.529 Gb, respectively). These results suggest complex relationship between genome size and TE content across Chilopoda. Since assembly contiguity can affect the recovery of long and nested repeats (notably LTRs), we investigated whether TE coverage correlated with assembly contiguity (N50). Correlations are weak to moderate and vary among clades (\u003cb\u003eSupplementary Fig.\u0026nbsp;4\u003c/b\u003e), indicating that assembly fragmentation alone does not explain the observed variation in repeat content.\u003c/p\u003e \u003cp\u003eOverall, our results highlight a variable contribution of TEs to genome size within Myriapoda and more specifically within Chilopoda. These differences between Diplopoda and Chilopoda suggest distinct dynamics in TE evolution and genome architecture across these taxa. To better understand these patterns, we next examined the evolutionary dynamics of TE families across species.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec13\" class=\"Section2\"\u003e \u003ch2\u003eEvolution of transposable elements\u003c/h2\u003e \u003cp\u003eTo investigate TE evolutionary dynamics across Myriapoda, we examined TE sequence divergence using Kimura substitution level (repeat landscape) plots (Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003e). These profiles approximate the age distribution of TE copies within each genome and highlight lineage-specific episodes of transposition, including recent bursts (low divergence) and older waves of accumulation (higher divergence).\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eAcross Diplopoda, repeat landscapes are generally dominated by TIR elements and a substantial fraction of unclassified repeats (Unknown), with broadly similar, unimodal shapes peaking at intermediate divergence levels (roughly\u0026thinsp;~\u0026thinsp;10\u0026ndash;25%), consistent with older or more gradual accumulation rather than extreme very recent bursts. This shared pattern is particularly evident within Julidae, which display closely comparable distributions, suggesting conserved repeat dynamics within this lineage. However, a subset of diplopods stands out by showing stronger contributions of retrotransposons: LINE-rich profiles are especially evident in \u003cem\u003eJulidae sp. jj 2019\u003c/em\u003e, \u003cem\u003eA. acrotrifoliolatus\u003c/em\u003e and \u003cem\u003eT. corallinus\u003c/em\u003e.\u003c/p\u003e \u003cp\u003eSpecies-specific signals are also apparent in several genomes. \u003cem\u003eC. punctatus\u003c/em\u003e exhibits two distinct peaks associated with LTR elements, consistent with multiple past expansion events of these retrotransposons. Likewise, \u003cem\u003eNanogona polydesmoides\u003c/em\u003e exhibits two distinct peaks associated with Helitron elements, indicating past expansion events of rolling-circle transposons in this lineage. Similarly, \u003cem\u003eH. holstii\u003c/em\u003e displays a clear low-divergence peak corresponding to Maverick elements, revealing a lineage-specific expansion of these large DNA transposons that is not observed at comparable levels in closely related taxa. In addition, a SINE peak at approximately 20% divergence is observed exclusively in \u003cem\u003eT. corallinus\u003c/em\u003e, while \u003cem\u003eC. punctatus\u003c/em\u003e shows evidence of a relatively recent expansion of PLE elements.\u003c/p\u003e \u003cp\u003eWithin Chilopoda, repeat landscapes are markedly more heterogeneous, revealing strong differences among orders and species. Several taxa show pronounced recent LTR retrotransposon expansions, with large peaks at very low divergence levels. This pattern is particularly striking in \u003cem\u003eS. acuminata\u003c/em\u003e and \u003cem\u003eS. maritima\u003c/em\u003e, both of which exhibit strong LTR-dominated signals consistent with recent or ongoing TE activity. The comparison between the two available assemblies of \u003cem\u003eS. acuminata\u003c/em\u003e further shows that the chromosome-level assembly contains a much stronger low-divergence signal than the contig-level assembly, indicating improved recovery of recent repetitive insertions in the more contiguous genome assembly.\u003c/p\u003e \u003cp\u003eOther Geophilomorpha species display broader divergence profiles with less pronounced recent peaks, suggesting either older accumulation or reduced recent TE activity relative to other chilopod groups. Nevertheless, species-level differences remain visible; for example, \u003cem\u003eStrigamia crassipes\u003c/em\u003e shows increased contributions of Helitron elements in the intermediate divergence classes.\u003c/p\u003e \u003cp\u003eLithobiomorpha species display comparatively strong low-divergence signals involving several TE classes, including LINEs and large DNA elements, consistent with recent TE accumulation. For \u003cem\u003eL. variegatus\u003c/em\u003e, we can observe a recent or sustained activity of Maverick elements. These patterns are in agreement with the high TE copy numbers observed in these large genomes and indicate active or recent TE proliferation in this lineage. Recent or ongoing expansions are also visible in the other large genomes of Chilopoda, namely \u003cem\u003eT. tuberculata\u003c/em\u003e (Scutigeromorpha) and the Scolopendromorpha \u003cem\u003eS. cretica\u003c/em\u003e and \u003cem\u003eR. immarginata\u003c/em\u003e, with a predominant expansion of TIRs. Conversely, the Scolopendromorpha \u003cem\u003eC. parisi\u003c/em\u003e, whose genome size is much smaller, shows very little recent activity.\u003c/p\u003e \u003cp\u003eOverall, repeat landscapes reveal both group-level similarities and species-specific bursts of activity across Myriapoda. Diplopod genomes generally show more homogeneous and older TE accumulation patterns, whereas chilopod genomes display greater variability, with several lineages exhibiting strong recent TE expansions driven by distinct TE classes. These results highlight that TE evolutionary histories differ substantially among myriapod lineages and often involve lineage-specific expansions of particular TE families.\u003c/p\u003e \u003c/div\u003e"},{"header":"Discussion","content":"\u003cdiv id=\"Sec15\" class=\"Section2\"\u003e \u003ch2\u003eAdvantages of RE annotation approach\u003c/h2\u003e \u003cp\u003eThe use of a unified and integrative annotation strategy enables comparisons of repeat composition across myriapod genomes, reducing methodological biases that often complicate cross-study interpretations. Importantly, applying a standardized annotation workflow across all analyzed genomes produces harmonized annotation files and analytical outputs, facilitating reproducible comparison.\u003c/p\u003e \u003cp\u003eThe EXOGAP framework relies on \u003cem\u003ede novo\u003c/em\u003e repeat discovery using RepeatModeler2, followed by systematic refinement of repeat libraries using MCHelper prior to genome masking. This strategy is particularly valuable for non-model organisms, where repeat diversity is often poorly represented in existing databases and assemblies may remain fragmented. MCHelper refines \u003cem\u003ede novo\u003c/em\u003e libraries by identifying gene-related sequences that may otherwise be retained as repeats, thereby reducing potential false positives. In addition, it integrates similarity searches, conserved domain detection, and structural characteristics to improve repeat classification. This refinement step also frequently extends consensus sequences predicted by RepeatModeler2, resulting in more complete repeat families and improving downstream genome annotation. In particular, the refined libraries enable a clearer distinction between different orders within Class II transposable elements. By improving the consistency and resolution of repeat classification, our approach provides a more detailed view of repeat composition across myriapod genomes.\u003c/p\u003e \u003cp\u003eTo date, few studies have focused on the REs of myriapods. Petersen et al. [\u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e], in their pioneering comparative study on arthropods, analyzed 73 arthropod genomes, primarily from insects (62 genomes), with only 11 genomes from other arthropod groups. This study was the first to include a myriapod genome (\u003cem\u003eS. maritima\u003c/em\u003e). Qu et al. [\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e] conducted the first comparative genomic study focusing exclusively on myriapods, analyzing the first three available myriapod genomes: \u003cem\u003eS. maritima\u003c/em\u003e, \u003cem\u003eH. holstii\u003c/em\u003e, and \u003cem\u003eT. corallinus\u003c/em\u003e. A second comparative genomic study was conducted by So et al. [\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e], comprising six additional genomes. Compared to the classical RepeatModeler\u0026ndash;RepeatMasker approach used in these pioneering studies, the combination of RepeatModeler and MCHelper for library construction improves the classification of repetitive elements (Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e7\u003c/span\u003e). Across most genomes examined, repeat annotations obtained here result in higher estimates of total TE coverage compared with previous studies, often accompanied by a reduction in the proportion of unclassified elements. However, the most notable improvement concerns the identification of specific TE. In particular, Class II DNA transposons and LTR retrotransposons are consistently recovered at substantially higher levels than previously reported, sometimes revealing several-fold increases in coverage.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec16\" class=\"Section2\"\u003e \u003ch2\u003eImpact of technical limitations on results\u003c/h2\u003e \u003cp\u003eIdentifying and accurately annotating TEs remains a significant challenge, particularly in fragmented genome assemblies. These differences are illustrated by the comparison between two \u003cem\u003eS. acuminata\u003c/em\u003e assemblies: a fragmented assembly obtained from Illumina reads and a chromosome-level assembly based on long read sequencing. The chromosome-level assembly shows only a slightly higher TE load (0.46\u0026nbsp;million copies compared with 0.35\u0026nbsp;million in the contig-level assembly), and the relative contributions of the different repeat orders remain broadly similar between assemblies. In contrast, TE coverage differs markedly, increasing from 35.4% in the contig-level assembly to 58.4% in the chromosome-level assembly. This indicates that although our approach efficiently detects the presence and diversity of TE families, many copies remain fragmented in lower-quality assemblies and therefore do not fully contribute to coverage estimates.\u003c/p\u003e \u003cp\u003eMore generally, the significant \"unclassified\" proportion of TEs in assemblies, including chromosome-level assemblies, underscores the ongoing challenges associated with TE classification in non-model species, potentially obscuring the true genomic contributions of DNA transposons, LTRs, LINEs, and SINEs. An additional challenge arises from the difficulty of accurately assembling satellite DNA. These regions are notoriously difficult to assemble, particularly in genomes sequenced with short-read technologies. Consequently, the relative contribution of satellite DNA to the overall genomic landscape is difficult to estimate. These findings emphasize the need for improved assembly strategies and annotation methods to achieve a more comprehensive characterization of TEs and satellite DNAs, especially in fragmented genomes.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec17\" class=\"Section2\"\u003e \u003ch2\u003eKey findings in TE dynamics across Myriapoda species\u003c/h2\u003e \u003cp\u003eOur study highlights the significant variation in TE abundance, composition, and contribution to genome size across Myriapoda species. While TIR and LTR elements dominate the genomes of most Myriapoda species, some species, particularly those with large genomes, are also rich in LINEs. For instance, LINEs account for 29.6% of the \u003cem\u003eA. acrotrifoliolatus\u003c/em\u003e genome. Within the Diplopoda, we observe relatively consistent TE compositions, especially within the Julida group, which share a similar evolutionary history, resulting in comparable TE profiles across species. However, certain Diplopoda species exhibit distinctive TE profiles. \u003cem\u003eT. corallinus\u003c/em\u003e is characterized by a high proportion of SINEs (9% of TE coverage), showing unique evolutionary trajectories compared to other Myriapoda species. Meanwhile, \u003cem\u003eH. holstii\u003c/em\u003e exhibits an increased presence of Maverick elements. This pattern contrasts with the broader diversity seen in Chilopoda, where TE compositions are more variable, influenced by both TIR and LTR elements. Recent or ongoing expansions of TIR elements are especially important in the large genomes of Scolopendromorpha, while recent bursts of LTR elements play a key role in species such as \u003cem\u003eS. maritima\u003c/em\u003e and \u003cem\u003eS. acuminata\u003c/em\u003e.\u003c/p\u003e \u003cp\u003eThis variation in TE composition suggests that the dynamics of REs may be shaped by distinct evolutionary pressures within different Myriapoda subgroups. Notably, genome size is strongly correlated with both TE load and TE coverage in Diplopoda, reflecting the expected pattern of larger genomes harboring more TEs. In contrast, Chilopoda exhibits more complex relationships, with genome size strongly correlated to TE load but moderately with TE coverage. Indeed, species like \u003cem\u003eS. acuminata\u003c/em\u003e and \u003cem\u003eS. maritima\u003c/em\u003e display comparable or even greater TE coverage than larger genomes like those of \u003cem\u003eL. variegatus\u003c/em\u003e and \u003cem\u003eT. tuberculata.\u003c/em\u003e This may be attributed to the recent expansion of LTR elements in these two \u003cem\u003eStrigamia\u003c/em\u003e species. More broadly, our study highlights the variability of TE dynamics across Myriapods, and particularly within Chilopoda, with the genomes of some species being shaped by recent or ongoing TE expansions. This may suggest lineage-specific shifts in TE regulation, recent TE invasion mediated by horizontal transfer or demographic factors limiting the efficiency of purifying selection against newly inserted elements in some species.\u003c/p\u003e \u003cp\u003eThe repeatome analysis revealed that nearly all known TE superfamilies are represented across Myriapoda species, though their abundance varies significantly. For example, the DIRS superfamily is more abundant in Chilopoda, while RTE elements are more prominent in Diplopoda. Several relatively rare families or subfamilies (e.g., Helitron, Penelope, and various groups related to MITE/Kolobok/Ginger/Zator) display mosaic distributions across species. Such patterns may reflect very recent lineage-specific activity, multiple independent losses, or limitations in the assignment of highly divergent TEs. These families therefore represent promising candidates for dedicated analyses (e.g., transposase or reverse transcriptase phylogenies, insertion dating) aimed at disentangling the underlying evolutionary scenarios.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec18\" class=\"Section2\"\u003e \u003ch2\u003eComparison with other arthropod groups\u003c/h2\u003e \u003cp\u003eThere is no clear pattern of conservation of REs across the entire arthropod clade, making comparisons challenging. The lack of a standardized classification of REs further complicates direct comparisons between species and groups. However, our study highlights the remarkable diversity in the distribution of REs in myriapods, which aligns with previous findings in other arthropods [\u003cspan citationid=\"CR53\" class=\"CitationRef\"\u003e53\u003c/span\u003e]. We show that myriapod genomes present a rich diversity of TE families, with few entirely absent: Casposons, typically confined to bacteria and archaea [\u003cspan citationid=\"CR54\" class=\"CitationRef\"\u003e54\u003c/span\u003e]; IR4 elements, documented solely in \u003cem\u003eCaenorhabditis elegans;\u003c/em\u003e VIPER elements [\u003cspan citationid=\"CR55\" class=\"CitationRef\"\u003e55\u003c/span\u003e], associated with Kinetoplastids and notably, Novosib elements, identified exclusively in certain insect species. Interestingly, SINE retrotransposons present across all Insect orders [\u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e] are largely absent in myriapods, with the notable exception of \u003cem\u003eT. corallinus\u003c/em\u003e.\u003c/p\u003e \u003cp\u003eWe observed notable differences in TE coverage and composition between Myriapods and other Arthropods. Myriapods exhibit a TE coverage ranging from 16% to 81% which is higher than that of chelicerates, where TE coverage does not exceed 40% [\u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e]. However, this coverage is lower compared to certain crustaceans with large genomes; for instance, the genome of \u003cem\u003eParalithodes platypus\u003c/em\u003e (4.8 Gb) has a TE coverage of 78.89% [\u003cspan citationid=\"CR56\" class=\"CitationRef\"\u003e56\u003c/span\u003e]. Moreover, myriapod genomes are primarily characterized by a strong contribution of DNA transposons, particularly terminal inverted repeat (TIR) elements, which dominate TE composition in most analyzed species. In contrast, Class I retrotransposons, especially LTR elements, show highly variable contributions and become prominent only in certain lineages, notably among some chilopods, without consistently dominating TE repertoires across the group.\u003c/p\u003e \u003cp\u003eThis pattern differs not only from many insect genomes, where LINEs or LTR retrotransposons frequently constitute the largest TE fractions, but also from chelicerates. In chelicerates, TE composition appears highly heterogeneous across species, with no consistent dominance of a single TE class, although DNA transposons often represent an important component. By contrast, myriapods display a more consistent predominance of TIR elements across species, suggesting more homogeneous large-scale TE dynamics within the group.\u003c/p\u003e \u003cp\u003eTogether, these observations indicate that myriapods possess a distinctive TE landscape in which DNA transposons and lineage-specific retrotransposon expansions jointly shape genome architecture. This combination likely contributes to the diversity of genome sizes and evolutionary trajectories observed across Myriapoda.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec19\" class=\"Section2\"\u003e \u003ch2\u003eFuture prospects\u003c/h2\u003e \u003cp\u003eAdvancing our understanding of TEs in Myriapoda and other arthropods faces several challenges. A significant limitation is the persistent presence of unclassified REs which underscores the need for improved TEs classification techniques. One potential solution lies in integrating advanced computational tools, such as machine learning approaches like DeepTE [\u003cspan citationid=\"CR57\" class=\"CitationRef\"\u003e57\u003c/span\u003e], TEClass2 [\u003cspan citationid=\"CR58\" class=\"CitationRef\"\u003e58\u003c/span\u003e], Terrier [\u003cspan citationid=\"CR59\" class=\"CitationRef\"\u003e59\u003c/span\u003e], TERL [\u003cspan citationid=\"CR60\" class=\"CitationRef\"\u003e60\u003c/span\u003e], and the newer framework CREATE [\u003cspan citationid=\"CR61\" class=\"CitationRef\"\u003e61\u003c/span\u003e] show promise by learning sequence features beyond similarity-based methods. However, these approaches generally rely on training datasets that do not fully capture the diversity of transposable elements across taxa, which can limit classification accuracy for highly divergent or lineage-specific repeats [\u003cspan citationid=\"CR59\" class=\"CitationRef\"\u003e59\u003c/span\u003e]. Moreover, some tools assign only broad TE classes unless retrained on user-provided data. As these methods are still relatively recent, broader validation across diverse genomes will be necessary, and classification of degraded or poorly characterized repeats remains challenging. Another crucial step is to expand genomic databases such as Dfam [\u003cspan citationid=\"CR62\" class=\"CitationRef\"\u003e62\u003c/span\u003e]. Although Dfam now includes thousands of species, representation remains uneven across major taxonomic groups \u0026mdash; notably, Myriapoda are not yet represented in this database.\u003c/p\u003e \u003cp\u003eIncreasing the availability of high-quality genome assemblies, particularly those generated with long-read sequencing technologies, represents another important research avenue. Long-read assemblies enable the detection of approximately 36% more REs compared to short-read technologies, with LTRs showing a remarkable 162% increase in detection rates [\u003cspan citationid=\"CR63\" class=\"CitationRef\"\u003e63\u003c/span\u003e]. Efforts to generate such assemblies are essential for improving TE characterization.\u003c/p\u003e \u003cp\u003eAddressing taxonomic gaps in genomic data is equally critical. The Symphyla and Pauropoda classes of Myriapoda, for instance, remain unrepresented in current genomic studies. Generating high-quality genome assemblies for these groups would not only fill this gap but also provide a more complete picture of TE diversity and dynamics within Myriapoda. This, in turn, would lay the groundwork for broader comparative analyses.\u003c/p\u003e \u003cp\u003eExpanding the scope of research to include a wider range of arthropod genomes would further enhance our understanding of lineage-specific trends and evolutionary patterns in TEs. Moreover, adopting a standardized analytical framework across studies would enable more meaningful comparisons and facilitate the identification of both shared features and unique adaptations across taxa, ultimately advancing the field significantly.\u003c/p\u003e \u003c/div\u003e"},{"header":"Abbreviations","content":"\u003cdiv class=\"DefinitionList\"\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eCont.\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003econtig\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eChrom.\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003echromosome\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eEXOGAP\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eExotic Organism Genome Annotation Pipeline\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eLINE\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eLong Interspersed Nuclear Elements\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eLTR\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eLong Terminal Repeat\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003ePLE\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003ePenelope like Element\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eRE\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eRepetitive Elements\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eTE\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eTransposable Element\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eTIR\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eTerminal Inverted Repeat\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eTR\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eTandem Repeat\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eSINE\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eShort Interspersed Nuclear Elements\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003c/div\u003e"},{"header":"Declarations","content":" \u003cp\u003e \u003cstrong\u003eEthics approval and consent to participate\u003c/strong\u003e \u003cp\u003eNot applicable.\u003c/p\u003e \u003c/p\u003e \u003cp\u003e \u003cstrong\u003eConsent for publication\u003c/strong\u003e \u003cp\u003eNot applicable.\u003c/p\u003e \u003c/p\u003e\u003cp\u003e \u003ch2\u003eCompeting interests\u003c/h2\u003e \u003cp\u003eThe authors declare no competing interests.\u003c/p\u003e \u003c/p\u003e\u003ch2\u003eFunding\u003c/h2\u003e \u003cp\u003eDM was supported by the French ministry of higher education and research and the doctoral school of Life Science of the University of Strasbourg. GC, CS, RL MB were supported through Landes-Offensive zur Entwicklung Wissenschaftlich-\u0026ouml;konomischer Exzellenz (LOEWE) Program of the Hessian Ministry of Higher Education, Research, Science and the Arts through the LOEWE/1/10/519/03/03.001(0014)/52 project (LOEWE Centre for Translational Biodiversity Genomics - LOEWE-TBG).\u003c/p\u003e\u003ch2\u003eAuthor Contribution\u003c/h2\u003e\u003cp\u003eOL and MB designed the study. GM, CS, PD, RL and MB generated much of the genomic data used in this study. DM and AK developed the annotation pipeline. DM analyzed the data. DM and OL interpreted data. DM and OL drafted the work and JT revised it. All authors reviewed the manuscript and agreed to the content.\u003c/p\u003e\u003ch2\u003eAcknowledgement\u003c/h2\u003e\u003cp\u003eWe thank the members of the BiGEst-ICube platform for their assistance and the Soil Invertebrate Genome Initiative (SIGI) (https://tbg.senckenberg.de/sigi/) consortium for helpful discussions.\u003c/p\u003e\u003ch2\u003eData Availability\u003c/h2\u003e\u003cp\u003eThe EXOGAP pipeline is publicly available on GitHub at [https://github.com/dorinemerlat/exogap](https:/github.com/dorinemerlat/exogap) . Genome assemblies analyzed in this study are available on NCBI Genomes database, with accession numbers provided in Materials and Methods. The *de novo* TE libraries and corresponding annotation files generated in this study have been deposited in Zenodo (https://doi.org/10.5281/zenodo.18695040).\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\u003cli\u003e\u003cspan\u003eMarek PE, Shear WA, Myriapods. Curr Biol. 2022;32:R1294\u0026ndash;6. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1016/j.cub.2022.09.058\u003c/span\u003e\u003cspan address=\"10.1016/j.cub.2022.09.058\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eEuropean Commission. Joint Research Centre. Global soil biodiversity atlas. LU: Publications Office; 2016. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.2788/799182\u003c/span\u003e\u003cspan address=\"10.2788/799182\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eSierwald P, Bond JE. Current Status of the Myriapod Class Diplopoda (Millipedes): Taxonomic Diversity and Phylogeny. Annu Rev Entomol. 2007;52:401\u0026ndash;20. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1146/annurev.ento.52.111805.090210\u003c/span\u003e\u003cspan address=\"10.1146/annurev.ento.52.111805.090210\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eMinelli A. The Myriapoda: Treatise on Zoology - Anatomy, Taxonomy, Biology. 1st ed. Leiden: BRILL; 2011.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eMarek PE, Buzatto BA, Shear WA, Means JC, Black DG, Harvey MS, et al. The first true millipede\u0026mdash;1306 legs long. Sci Rep. 2021;11:23126. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1038/s41598-021-02447-0\u003c/span\u003e\u003cspan address=\"10.1038/s41598-021-02447-0\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eT\u0026oacute;th Z, Hornung E. Taxonomic and Functional Response of Millipedes (Diplopoda) to Urban Soil Disturbance in a Metropolitan Area. Insects. 2019;11:25. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.3390/insects11010025\u003c/span\u003e\u003cspan address=\"10.3390/insects11010025\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eJoly F-X, Coq S, Coulis M, David J-F, H\u0026auml;ttenschwiler S, Mueller CW, et al. Detritivore conversion of litter into faeces accelerates organic matter turnover. Commun Biol. 2020;3:660. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1038/s42003-020-01392-4\u003c/span\u003e\u003cspan address=\"10.1038/s42003-020-01392-4\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eUndheim EAB, King GF. On the venom system of centipedes (Chilopoda), a neglected group of venomous animals. Toxicon. 2011;57:512\u0026ndash;24. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1016/j.toxicon.2011.01.004\u003c/span\u003e\u003cspan address=\"10.1016/j.toxicon.2011.01.004\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eEdgecombe GD, Giribet G. Evolutionary Biology of Centipedes (Myriapoda: Chilopoda). Annu Rev Entomol. 2007;52:151\u0026ndash;70. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1146/annurev.ento.52.110405.091326\u003c/span\u003e\u003cspan address=\"10.1146/annurev.ento.52.110405.091326\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eScheller U. A reclassification of the Pauropoda (Myriapoda). Int J Myriapodology. 2008;1:1\u0026ndash;38. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1163/187525408X316730\u003c/span\u003e\u003cspan address=\"10.1163/187525408X316730\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eGao Y, Bu Y. Two new species of the genus Samarangopus and the first record of Eurypauropus japonicus (Arthropoda, Myriapoda, Pauropoda, Eurypauropodidae) from China. ZK. 2023;1165:137\u0026ndash;54. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.3897/zookeys.1165.102936\u003c/span\u003e\u003cspan address=\"10.3897/zookeys.1165.102936\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eBrewer MS, Sierwald P, Bond JE. Millipede Taxonomy after 250 Years: Classification and Taxonomic Practices in a Mega-Diverse yet Understudied Arthropod Group. PLoS ONE. 2012;7:e37240. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1371/journal.pone.0037240\u003c/span\u003e\u003cspan address=\"10.1371/journal.pone.0037240\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eChipman AD, Ferrier DEK, Brena C, Qu J, Hughes DST, Schr\u0026ouml;der R, et al. The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima. PLoS Biol. 2014;12:e1002005. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1371/journal.pbio.1002005\u003c/span\u003e\u003cspan address=\"10.1371/journal.pbio.1002005\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eQu Z, Nong W, So WL, Barton-Owen T, Li Y, Leung TCN, et al. Millipede genomes reveal unique adaptations during myriapod evolution. PLoS Biol. 2020;18:e3000636. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1371/journal.pbio.3000636\u003c/span\u003e\u003cspan address=\"10.1371/journal.pbio.3000636\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eSo WL, Nong W, Xie Y, Baril T, Ma H, Qu Z, et al. Myriapod genomes reveal ancestral horizontal gene transfer and hormonal gene loss in millipedes. Nat Commun. 2022;13:3010. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1038/s41467-022-30690-0\u003c/span\u003e\u003cspan address=\"10.1038/s41467-022-30690-0\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eCollins G, Schneider C, Boštjančić LL, Burkhardt U, Christian A, Decker P, et al. The MetaInvert soil invertebrate genome resource provides insights into below-ground biodiversity and evolution. Commun Biol. 2023;6:1241. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1038/s42003-023-05621-4\u003c/span\u003e\u003cspan address=\"10.1038/s42003-023-05621-4\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eBiscotti MA, Olmo E, Heslop-Harrison JS. Repetitive DNA in eukaryotic genomes. Chromosome Res. 2015;23:415\u0026ndash;20. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1007/s10577-015-9499-z\u003c/span\u003e\u003cspan address=\"10.1007/s10577-015-9499-z\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eT\u0026oslash;rresen OK, Star B, Mier P, Andrade-Navarro MA, Bateman A, Jarnot P, et al. Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases. Nucleic Acids Res. 2019;47:10994\u0026ndash;1006. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1093/nar/gkz841\u003c/span\u003e\u003cspan address=\"10.1093/nar/gkz841\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eUnderwood CJ, Henderson IR, Martienssen RA. Genetic and epigenetic variation of transposable elements in Arabidopsis. Curr Opin Plant Biol. 2017;36:135\u0026ndash;41. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1016/j.pbi.2017.03.002\u003c/span\u003e\u003cspan address=\"10.1016/j.pbi.2017.03.002\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eQin S, Jin P, Zhou X, Chen L, Ma F. The Role of Transposable Elements in the Origin and Evolution of MicroRNAs in Human. PLoS ONE. 2015;10:e0131365. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1371/journal.pone.0131365\u003c/span\u003e\u003cspan address=\"10.1371/journal.pone.0131365\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eWicker T, Sabot F, Hua-Van A, Bennetzen JL, Capy P, Chalhoub B, et al. A unified classification system for eukaryotic transposable elements. Nat Rev Genet. 2007;8:973\u0026ndash;82. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1038/nrg2165\u003c/span\u003e\u003cspan address=\"10.1038/nrg2165\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eMakałowski W, Gotea V, Pande A, Makałowska I. Transposable Elements: Classification, Identification, and Their Use As a Tool For Comparative Genomics. In: Anisimova M, editor. Evolutionary Genomics. New York, NY: Springer New York; 2019. pp. 177\u0026ndash;207. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1007/978-1-4939-9074-0_6\u003c/span\u003e\u003cspan address=\"10.1007/978-1-4939-9074-0_6\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eHavecker ER, Gao X, Voytas DF. The diversity of LTR retrotransposons. Genome Biol. 2004;5:225. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1186/gb-2004-5-6-225\u003c/span\u003e\u003cspan address=\"10.1186/gb-2004-5-6-225\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eBiedler J. Non-LTR Retrotransposons in the African Malaria Mosquito, Anopheles gambiae: Unprecedented Diversity and Evidence of Recent Activity. Mol Biol Evol. 2003;20:1811\u0026ndash;25. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1093/molbev/msg189\u003c/span\u003e\u003cspan address=\"10.1093/molbev/msg189\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eMills RE, Bennett EA, Iskow RC, Devine SE. Which transposable elements are active in the human genome? Trends Genet. 2007;23:183\u0026ndash;91. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1016/j.tig.2007.02.006\u003c/span\u003e\u003cspan address=\"10.1016/j.tig.2007.02.006\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eArkhipova IR. Distribution and Phylogeny of Penelope-Like Elements in Eukaryotes. Syst Biol. 2006;55:875\u0026ndash;85. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1080/10635150601077683\u003c/span\u003e\u003cspan address=\"10.1080/10635150601077683\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003ePoulter RTM, Butler MI. Tyrosine Recombinase Retrotransposons and Transposons. Microbiol Spectr. 2015;3. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1128/microbiolspec.MDNA3-0036-2014\u003c/span\u003e\u003cspan address=\"10.1128/microbiolspec.MDNA3-0036-2014\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e. 3.2.07.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eKojima KK, Jurka J. Crypton transposons: identification of new diverse families and ancient domestication events. Mob DNA. 2011;2:12. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1186/1759-8753-2-12\u003c/span\u003e\u003cspan address=\"10.1186/1759-8753-2-12\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eThomas J, Pritham EJ. Helitrons, the Eukaryotic Rolling-circle Transposable Elements. Microbiol Spectr. 2015;3. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1128/microbiolspec.MDNA3-0049-2014\u003c/span\u003e\u003cspan address=\"10.1128/microbiolspec.MDNA3-0049-2014\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e. 3.4.03.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003ePritham EJ, Feschotte C. Massive amplification of rolling-circle transposons in the lineage of the bat Myotis lucifugus. Proc Natl Acad Sci USA. 2007;104:1895\u0026ndash;900. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1073/pnas.0609601104\u003c/span\u003e\u003cspan address=\"10.1073/pnas.0609601104\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003ePritham EJ, Putliwala T, Feschotte C. Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses. Gene. 2007;390:3\u0026ndash;17. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1016/j.gene.2006.08.008\u003c/span\u003e\u003cspan address=\"10.1016/j.gene.2006.08.008\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eHannan AJ. Expanding horizons of tandem repeats in biology and medicine: Why \u0026lsquo;genomic dark matter\u0026rsquo; matters. Emerg Top Life Sci. 2023;7:239\u0026ndash;47. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1042/ETLS20230075\u003c/span\u003e\u003cspan address=\"10.1042/ETLS20230075\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003ePetersen M, Armis\u0026eacute;n D, Gibbs RA, Hering L, Khila A, Mayer G, et al. Diversity and evolution of the transposable element repertoire in arthropods with particular reference to insects. BMC Evol Biol. 2019;19:11. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1186/s12862-018-1324-9\u003c/span\u003e\u003cspan address=\"10.1186/s12862-018-1324-9\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eSchoch CL, Ciufo S, Domrachev M, Hotton CL, Kannan S, Khovanskaya R, et al. NCBI Taxonomy: a comprehensive update on curation, resources and tools. Database. 2020;2020:baaa062. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1093/database/baaa062\u003c/span\u003e\u003cspan address=\"10.1093/database/baaa062\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eTegenfeldt F, Kuznetsov D, Manni M, Berkeley M, Zdobnov EM, Kriventseva EV. OrthoDB and BUSCO update: annotation of orthologs with wider sampling of genomes. Nucleic Acids Res. 2025;53:D516\u0026ndash;22. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1093/nar/gkae987\u003c/span\u003e\u003cspan address=\"10.1093/nar/gkae987\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eKriventseva EV, Kuznetsov D, Tegenfeldt F, Manni M, Dias R, Sim\u0026atilde;o FA, et al. OrthoDB v10: sampling the diversity of animal, plant, fungal, protist, bacterial and viral genomes for evolutionary and functional annotations of orthologs. Nucleic Acids Res. 2019;47:D807\u0026ndash;11. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1093/nar/gky1053\u003c/span\u003e\u003cspan address=\"10.1093/nar/gky1053\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eEdgecombe GD, Sivell D et al. Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life programme, Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective,. The genome sequence of the centipede Strigamia acuminata (Leach, 1816). Wellcome Open Res. 2023;8:420. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.12688/wellcomeopenres.19941.1\u003c/span\u003e\u003cspan address=\"10.12688/wellcomeopenres.19941.1\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eThe Darwin Tree of Life Project Consortium, Blaxter M, Mieszkowska N, Di Palma F, Holland P, Durbin R, et al. Sequence locally, think globally: The Darwin Tree of Life Project. Proc Natl Acad Sci USA. 2022;119:e2115642118. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1073/pnas.2115642118\u003c/span\u003e\u003cspan address=\"10.1073/pnas.2115642118\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eEdgecombe GD, Crowley LM, Telfer MG, Hughes L et al. University of Oxford and Wytham Woods Genome Acquisition Lab, Natural History Museum Genome Acquisition Lab,. The genome sequence of the banded centipede, Lithobius variegatus Leach, 1814. Wellcome Open Res. 2025;10:285. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.12688/wellcomeopenres.24329.1\u003c/span\u003e\u003cspan address=\"10.12688/wellcomeopenres.24329.1\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eGregory J, Edgecombe S et al. GD, Natural History Museum Genome Acquisition Lab, Darwin Tree of Life Barcoding Collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team, Wellcome Sanger Institute Scientific Operations: Sequencing Operations,. The genome sequence of the millipede, Choneiulus palmatus (Nĕmec, 1895) (Julida: Blaniulidae). Wellcome Open Res. 2025;10:513. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.12688/wellcomeopenres.24885.1\u003c/span\u003e\u003cspan address=\"10.12688/wellcomeopenres.24885.1\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eEdgecombe GD, Crowley LM, Telfer MG et al. University of Oxford and Wytham Woods Genome Acquisiiton Lab, Darwin Tree of Life Barcoding collective, Wellcome Sanger Institute Tree of Life Management, Samples and Laboratory team,. The genome sequence of the club-tailed millipede, Cylindroiulus punctatus (Leach, 1816). Wellcome Open Res. 2025;10:256. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.12688/wellcomeopenres.24251.1\u003c/span\u003e\u003cspan address=\"10.12688/wellcomeopenres.24251.1\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eOwen C, Sivell O, Sivell D, Twitchett RJ, Edgecombe GD et al. Natural History Museum Genome Acquisition Lab,. The genome sequence of the eyed flat-backed millipede, Nanogona polydesmoides (Leach, 1814). Wellcome Open Res. 2025;10:332. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.12688/wellcomeopenres.24341.1\u003c/span\u003e\u003cspan address=\"10.12688/wellcomeopenres.24341.1\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eFlynn JM, Hubley R, Goubert C, Rosen J, Clark AG, Feschotte C, et al. RepeatModeler2 for automated genomic discovery of transposable element families. Proc Natl Acad Sci USA. 2020;117:9451\u0026ndash;7. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1073/pnas.1921046117\u003c/span\u003e\u003cspan address=\"10.1073/pnas.1921046117\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eEllinghaus D, Kurtz S, Willhoeft U. LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformatics. 2008;9:18. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1186/1471-2105-9-18\u003c/span\u003e\u003cspan address=\"10.1186/1471-2105-9-18\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eOu S, Jiang N, LTR_retriever:. A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons. Plant Physiol. 2018;176:1410\u0026ndash;22. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1104/pp.17.01310\u003c/span\u003e\u003cspan address=\"10.1104/pp.17.01310\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eOrozco-Arias S, Sierra P, Durbin R, Gonz\u0026aacute;lez J. MCHelper automatically curates transposable element libraries across eukaryotic species. Genome Res. 2024;34:2256\u0026ndash;68. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1101/gr.278821.123\u003c/span\u003e\u003cspan address=\"10.1101/gr.278821.123\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eBao W, Kojima KK, Kohany O. Repbase Update, a database of repetitive elements in eukaryotic genomes. Mob DNA. 2015;6:11. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1186/s13100-015-0041-9\u003c/span\u003e\u003cspan address=\"10.1186/s13100-015-0041-9\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eBenson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27:573\u0026ndash;80. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1093/nar/27.2.573\u003c/span\u003e\u003cspan address=\"10.1093/nar/27.2.573\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eQuinlan AR, Hall IM. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 2010;26:841\u0026ndash;2. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1093/bioinformatics/btq033\u003c/span\u003e\u003cspan address=\"10.1093/bioinformatics/btq033\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eR Core Team. R: a language and environment for statistical computing. manual. Vienna, Austria: R Foundation for Statistical Computing; 2021.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eWickham H. ggplot2: Elegant Graphics for Data Analysis. New York, NY: Springer New York; 2009. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1007/978-0-387-98141-3\u003c/span\u003e\u003cspan address=\"10.1007/978-0-387-98141-3\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eGu Z, Eils R, Schlesner M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics. 2016;32:2847\u0026ndash;9. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1093/bioinformatics/btw313\u003c/span\u003e\u003cspan address=\"10.1093/bioinformatics/btw313\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eWu C, Lu J. Diversification of Transposable Elements in Arthropods and Its Impact on Genome Evolution. Genes. 2019;10:338. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.3390/genes10050338\u003c/span\u003e\u003cspan address=\"10.3390/genes10050338\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eKrupovic M, B\u0026eacute;guin P, Koonin EV. Casposons: mobile genetic elements that gave rise to the CRISPR-Cas adaptation machinery. Curr Opin Microbiol. 2017;38:36\u0026ndash;43. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1016/j.mib.2017.04.004\u003c/span\u003e\u003cspan address=\"10.1016/j.mib.2017.04.004\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eLorenzi HA, Robledo G, Levin MJ. The VIPER elements of trypanosomes constitute a novel group of tyrosine recombinase-enconding retrotransposons. Mol Biochem Parasitol. 2006;145:184\u0026ndash;94. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1016/j.molbiopara.2005.10.002\u003c/span\u003e\u003cspan address=\"10.1016/j.molbiopara.2005.10.002\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eRutz C, Bonassin L, Kress A, Francesconi C, Boštjančić LL, Merlat D, et al. Abundance and Diversification of Repetitive Elements in Decapoda Genomes. Genes. 2023;14:1627. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.3390/genes14081627\u003c/span\u003e\u003cspan address=\"10.3390/genes14081627\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eYan H, Bombarely A, Li S. DeepTE: a computational method for \u003cem\u003ede novo\u003c/em\u003e classification of transposons with convolutional neural network. Bioinformatics. 2020;36:4269\u0026ndash;75. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1093/bioinformatics/btaa519\u003c/span\u003e\u003cspan address=\"10.1093/bioinformatics/btaa519\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eBickmann L, Rodriguez M, Jiang X, Makalowski W. TEclass2: Classification of transposable elements using Transformers. 2023. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1101/2023.10.13.562246\u003c/span\u003e\u003cspan address=\"10.1101/2023.10.13.562246\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eTurnbull R, Young ND, Tescari E, Skerratt LF, Kosch TA. Terrier: a deep learning repeat classifier. Brief Bioinform. 2025;26:bbaf442. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1093/bib/bbaf442\u003c/span\u003e\u003cspan address=\"10.1093/bib/bbaf442\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eDa Cruz MHP, Domingues DS, Saito PTM, Paschoal AR, Bugatti PH. TERL: classification of transposable elements by convolutional neural networks. Brief Bioinform. 2021;22:bbaa185. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1093/bib/bbaa185\u003c/span\u003e\u003cspan address=\"10.1093/bib/bbaa185\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eQi Y, Chen Y, Wu Y, Guo Y, Gao M, Zhang F, et al. CREATE: a novel attention-based framework for efficient classification of transposable elements. Brief Bioinform. 2025;26:bbaf608. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1093/bib/bbaf608\u003c/span\u003e\u003cspan address=\"10.1093/bib/bbaf608\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eHubley R, Finn RD, Clements J, Eddy SR, Jones TA, Bao W, et al. The Dfam database of repetitive DNA families. Nucleic Acids Res. 2016;44:D81\u0026ndash;9. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1093/nar/gkv1272\u003c/span\u003e\u003cspan address=\"10.1093/nar/gkv1272\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003cli\u003e\u003cspan\u003eSproul JS, Hotaling S, Heckenhauer J, Powell A, Marshall D, Larracuente AM, et al. Analyses of 600\u0026thinsp;+\u0026thinsp;insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges. Genome Res. 2023;33:1708\u0026ndash;17. \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://doi.org/10.1101/gr.277387.122\u003c/span\u003e\u003cspan address=\"10.1101/gr.277387.122\" targettype=\"DOI\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/span\u003e\u003c/li\u003e \u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":false,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":false,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"Repetitive element, Transposable elements, Myriapoda, Genome evolution, Annotation","lastPublishedDoi":"10.21203/rs.3.rs-8918891/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8918891/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003ch2\u003eBackground\u003c/h2\u003e \u003cp\u003eTransposable elements (TEs) are major drivers of genome evolution, yet their diversity and dynamics remain poorly characterized in many non-model animal lineages, including Myriapoda. The recent expansion of genomic resources in this group now enables comparative analyses, but TE annotation remains challenging due to heterogeneous assembly qualities and the complexity of repeat landscapes.\u003c/p\u003e\u003ch2\u003eResults\u003c/h2\u003e \u003cp\u003eWe present a standardized comparative analysis of repetitive elements across 36 myriapod species, providing a comprehensive overview of TE abundance, composition, and activity. TE landscapes vary strongly among lineages, with TIR elements dominating most genomes, while LTR elements show lineage-specific expansions, particularly in several chilopods. Genome size correlates strongly with TE abundance in diplopods, whereas this relationship is weaker and more variable in chilopods, suggesting contrasting evolutionary dynamics across clades. Repeat divergence analyses further reveal signatures of recent TE activity, indicating that repeat-driven genome remodeling remains ongoing in myriapods.\u003c/p\u003e\u003ch2\u003eConclusion\u003c/h2\u003e \u003cp\u003eOur results demonstrate that genome size evolution in Myriapoda reflects lineage-specific TE dynamics and highlight the importance of standardized annotation for cross-species comparisons. We additionally provide an automated workflow for repeat annotation and visualization, enabling reproducible large-scale analyses of repeatomes in non-model organisms, and make this workflow publicly available at: \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://github.com/dorinemerlat/exogap\u003c/span\u003e\u003cspan address=\"https://github.com/dorinemerlat/exogap\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e.\u003c/p\u003e","manuscriptTitle":"Repetitive Elements in Myriapoda: Genomic Diversity and Evolution","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-03-04 19:27:51","doi":"10.21203/rs.3.rs-8918891/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"e4f8fa5e-a422-4a13-9704-cadead1eb8a7","owner":[],"postedDate":"March 4th, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2026-03-31T22:09:17+00:00","versionOfRecord":[],"versionCreatedAt":"2026-03-04 19:27:51","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8918891","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8918891","identity":"rs-8918891","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}