Machine learning based pan-plant analyses of transposable elements across 352 species illuminates genome evolution

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This study presents a comprehensive analysis of TEs across 558 high-quality plant genomes, encompassing 352 species from 221 genera across five phyla, ranging from algae to angiosperms. We identified over 460 million TEs and 67 million transposase domains, systematically assessing their impact on host genomes through gene domestication, noncoding RNA generation, and gene duplication. Our analysis revealed 1,258,230 genes domesticated from TEs, 1,165,059 ncRNAs originating from TEs, and 10,488,967 TE-induced gene duplications. These genes affect more than 2,805 function families, likely planning crucial roles at key stages of plant evolution. Using a machine learning-based framework, we uncovered 1,536 lineage-specific functional gene families significantly influenced by TEs, with enzymes and transcription factors being predominant. Notably, we elucidated the role of TEs in expanding transcription factor gene families and in facilitating potential horizontal gene transfer of synthase gene families. This study provides unprecedented insights into TE-driven plant evolution, demonstrating how TEs contributes to key innovations at various evolutionary stages. Our finding not only enhance understanding of plant genome dynamics but also offer valuable resources for crop improvement and synthetic biology, illumination both current knowledge and future potential of evolutionary processes. Transposable elements Genome evolution Plant Computational biology and bioinformatics Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Background Transposable elements (TEs) are DNA fragments that can move and amplify within the genome, and are believed to constitute one major type of “nature’s genetic engineer” in evolution 1 , 2 . They play a key role in genome function, speciation, and diversity 3 , 4 , shaping both individual genes and the entire genome. TEs were first discovered in the 1940s by Barbara McClintock 5 . Since then, numerous types of TEs have been identified in the genomes of both plants and animals 1 . TEs serve as an extraordinary source of evolutionary novelties and have been involved in the evolution of several important biological processes across eukaryotes 6 , 7 . As significant players in genome evolution, TEs can be activated under stress conditions, introducing novel structural variation in the insertion sites, which can lead to the generation of new genes and the modification of existing gene structures through the duplication, mobilization and recombination of gene fragments 8 – 10 . During the evolution of plants from lower to higher taxa, the functional diversity of genes markedly increased. However, the specific roles and impacts of TEs in this process—specifically how and where they exert their influence—remain largely unclear. TEs may act as reservoirs for generating new gene variants through recombination 11 , and they can also facilitate cellular functions by sharing transposase-coding regions 12 . By inserting themselves into protein-coding genes, TEs can affect genes 13 either by providing novel regulatory sequences 14 or by mutating the interrupted gene 12 . This process is known as ‘molecular domestication’ 15 , in which transposase genes acquire mutations so that their products (transposases, reverse transcriptases, integrases, coat proteins, etc.) no longer function in catalyzing transposition and instead evolve novel functions. Domesticated transposases have been identified from both forward genetic screens on the basis of phenotypes, and bioinformatic analyses of genome sequences 16 . TE domestication has been reported in both animals and plants. In the human genome, at least 50 genes have been domesticated from TEs 17 – 19 . In Arabidopsis thaliana , 7.8% of expressed genes contained sequences from TEs, whereas 1.2% had translation evidence suggesting the exonization of TEs 20 . Beyond the exaptation of the entire transposase, computational analyses have demonstrated that partial TE sequences have been incorporated into protein-coding genes. Chimeric transcripts between TEs and protein coding genes tend to be common 21 , 22 . Similarly, Class I Alu TEs in human are present in ∼10% of mature mRNAs 23 . Additionally, growing evidence indicates a close association of TEs with non-coding RNAs (ncRNAs), with a significant number of small ncRNAs originating from TEs 24 – 26 . The presence of domesticated TEs suggests that TEs may play an active role in gene evolution. However, larger-scale analyses are needed to better understand their specific contributions. TEs can sequester host genes, inducing their duplication and vertical transfer to descendants. Transposed duplication (TRD) generates a gene pair comprising of an ancestral locus and a novel locus, and is presumed to arise from distantly transposed duplication that occur via DNA-based or RNA-based mechanisms 27 , 28 . DNA transposons, such as packmules (rice) 29 , Helitrons (maize) 30 , and CACTA elements (sorghum) 31 , may relocate duplicated genes or gene segments to new chromosomal positions. RNA-based transposed duplication, often referred to as retrotransposition, typically creates a single-exon retrocopy from a multiexon parental gene by reverse transcription of a spliced messenger RNA. The expansion of gene families can often be attributed to specific modes of gene duplication 32 . For instance, DNA-based transposed duplications are prevalent among disease resistance gene homologs, indicating that there may be non-random, recurrent patterns in the origins of gene family members across diverse evolutionary lineages. These observations underscore the need for further investigation into this phenomenon. Moreover, identifying distantly transposed gene duplication at the genomic scale remains a challenging task. Currently, the classification of transposed duplication genes relies primarily on measuring the physical distance and exon count between duplicate genes 27 . However, this approach does not fully utilize the positional and sequence information provided by TEs. Therefore, comprehensive comparative genomics analyses are needed, encompassing both genes and TEs within and across species. The advancement of precise and cost-effective sequencing technologies, along with the practice of open data sharing, has led to a remarkable increase in accessible plant genome assemblies over the past decade. Currently, within the NCBI genome database, there exist 2,045 genome assemblies for plants at the chromosome-level or complete level, encompassing 517 genera and 945 species (accessed on June 20, 2024). The initial discovery of TEs was driven by their impact on phenotypes and their widespread presence in the maize genome 33 . Whole-genome sequencing reveals the involvement of TEs at the genomic structure level, providing insights into the functional degree of these TE sequences 1 . Although TEs play a significant role in shaping genomic structure and influencing phenotypic variation, much re 34 mains to be understood about those TEs that have undergone positive selection throughout the evolutionary history of plants. Extensive comparative genomic studies are beginning to shed light on the impact of TEs on plant evolution, including their contributions to genome architecture and their effects on gene expression and phenotypic diversity. The idea that genomes are constructed in a Lego-like manner from codons specifying protein domains dates back to McClintock’s observations. She noted that developmental patterns in maize varied due to the insertion and excision of chromosome segments, which she referred to as “controlling elements” 33 . The concept of exon shuffling as the source of diverse protein structures is another variation of this theme 35 , 36 . However, the impact of TEs on genomic genetic innovation has primarily been identified from forward genetic screens based on phenotypes, such as in Arabidopsis thaliana 37 , maize 34 , orange 38 , peas 39 and grape. Today, with the advent of large-scale sequencing projects and advancements in sequencing technology, the whole-genome assemblies of an increasing number of species have been published 40 – 43 . McClintock’s observations and hypotheses can be validated and refined through extensive comparative studies across species to systematically assessing the impact of TEs on functional genomics during plant evolution. In this study, we conducted pan-plant comparisons across 558 plant genomes, encompassing 352 species from 221 genera. We meticulously identified all TEs, traced their proliferation and dispersion in plant genomes, and assessed their overlap with other annotated genomic features to identify novel TE-associated genes and ncRNAs. Furthermore, through interspecies comparisons and functional analysis, we can evaluate the specific effects that TEs might have at different evolutionary stages, as well as how these effects emerge. Ultimately, this research aims to illuminate not only the current understanding but also the future potential of evolutionary processes. Results To comprehensively analyze the composition of transposable elements (TEs) across the plant kingdom and their impact on plant genomes, this study conducted a taxonomically focused survey of assembled genomes from public databases, including NCBI, Ensembl, CNCB, and Phytozome, along with relevant literature. We selected 558 high-quality genomes from 352 species for analysis, representing a broad spectrum of major plant groups, including algae, mosses, ferns, gymnosperms, and angiosperms (Table S1 ) . The project is divided into three main parts ( Fig. 1 A, Fig S1 A) : First, TE de novo annotation was performed on the 558 assembled genomes from 352 species, and the effects of TEs on genome structure and function were analyzed; Second, we examined the role of eight TE superfamilies in driving genetic innovation within plant genomes; Third, we investigated the impact of TEs on plant evolution. Effects of TEs on Plant Genomes De novo identification of TEs By employing EDTA 44 for de novo annotation of transposons across 532 genomes from 352 species, and utilizing EDTA annotations from 26 maize genomes downloaded from MaGDB 43 , this study analyzed a total of 539.50 Gb of genomic sequences. Among these, 330.90 Gb were identified as TE sequences (constituting 61.33%), and encompassing 461,915,455 transposons, including 256,444,665 (55.52%) Class I transposons (including Copia and Gypsy) and 201,301,619 (43.58%) class II transposons (including hAT, CACTA, PIF-Harbinger , Mutator, Tc1-Mariner , and Helitron ) ( Table S2 , Fig. 1 B ) . The proportion of transposons aligns with previous findings 45 , with a greater representation of class I transposon sequences, reflecting their contribution to genome size (Fig S1 B, Fig S1 C) . Furthermore, we annotated conserved domains associated with transposases via TransposonPSI 46 , identifying 67,851,836 transposon domains, which include 61,807,023 (91.09%) class I transposon domains and 6,044,813 (8.91%) class II transposon domains. The number of conserved domains for class II transposons is less than one-tenth that of class I transposons, indicating that class II transposons contain a greater proportion of nonautonomous elements than class I transposons do. TE-associated Genetic Components TE insertions can be neutral or even advantageous for the host, leading to long-term retention of TEs in the host genome. This phenomenon referred to as TE exaptation or TE domestication, is a process in which TEs become part of the regulatory and/or coding region of host genes and contribute to diverse phenotypes and important functions 47 . The spatial relationships between TEs and genes provide important evidence of how TEs shape gene evolution and drive genetic innovation. In this study, we systematically identified TEs and other genetic components (functional genes and ncRNAs) within genomes to analyze their sequence colocalization relationships ( Fig. 1 A ) , evaluating TE-associated genetic components across 352 plant species. This analysis led to the identification of 1,258,230 domesticated transposases (accounting for 4.90% of the total genes), 10,488,967 TE-induced gene duplications (accounting for 40.83% of the total genes), and 1,165,059 ncRNAs derived from TEs (accounting for 29.13% of the total ncRNAs) (Table S3 ). Figure 1 C illustrates three types of genetic innovations generated by TEs. Overall, TEs affected about half of the function genes and one-third of the ncRNAs, with TE-induced gene duplications constituting the largest proportion. Domesticated transposase-derived genes are more prevalent in ferns and gymnosperms, whereas their proportion is notably low in algae, while TE-associated ncRNAs are more abundant in monocots. TE- associated Genetic Function Innovation To further determine the impact of TEs on plant genome function, we performed cross-species comparisons and enrichment analyses of the identified TE-associated genetic components. Given that TE-associated genetic components are subject to natural selection and are vertically transmitted along evolutionary lineages 48 , three key characteristics emerged from our comparisons: First, if a gene family is associated with TEs and vertically transmitted, it will be significantly enriched among TE-associated genes. Second, if a gene family is derived from domesticated transposases or TE sequences, it will spread through lineages as plants evolve. Finally, if a gene family is amplified through transposition, the number of family members in different species should be highly correlated with the number of TE-induced family members duplications. Here, we conducted an enrichment analysis for each genetic function family, assessed the proportion of domesticated sources across all species and calculated the correlation between the total gene count and TE-mediated duplication genes (Table S4 ) . As shown in Fig. 1 D, the gene functional families significantly associated with TEs are clustered in the upper right corner of the scatter plot, with many family genes, indicating a synergistic effect of TEs on these functional genes. Additionally, we calculated the median gene counts of the top 20 enriched gene families for TE-associated genetic functional innovations across different plant populations, as shown in Fig. 1 E. As expected, most of these functional genes are related to chromatin, such as "nucleic acid binding, RNA-DNA hybrid ribonuclease, DNA integration, telomere maintenance, DNA helicase activity", etc. Overall, TEs can influence functional gene families through two dimensions: providing new domains and mediating duplication, with a synergistic effect between the two. Impact of TE Superfamilies The composition and transposition mechanisms of different TE superfamilies vary 49 , as do their host genome preferences (Fig S2 ) , which may lead to differences in the genetic innovations they mediate. To explore the potential roles of various TE superfamilies in evolutionary processes, we conducted additional statistical and enrichment analyses on TE-associated genetic components for each TE superfamily (Table S5 ) . ncRNAs Originating from TEs The emergence of ncRNAs from TEs is a crucial adaptive mechanism for plants survival. Research indicates that several ncRNAs are encoded by TEs or by endogenous genes that are likely derived from TEs 50 – 52 . Additionally, ncRNAs encoded by TEs can repress the proliferation of their originating TEs through sequence complementarity (i.e., TE silencing) 52 , 53 . To analyze the relationship between TEs and host ncRNAs, we conducted statistical and enrichment analyses on TE-origin ncRNAs. As shown in Fig. 2 A, Class II DNA accounts for more than 80% of TE-associated ncRNAs, with the Tc1-Mariner family being the most prevalent, accounting for approximately one-third of this total. We then performed a family enrichment analysis for ncRNAs related to each TE superfamily, using all TE-associated ncRNAs as a background. The top 10 significantly enriched ncRNA families were mapped to their corresponding TE superfamilies to create a network, as depicted in Fig. 2 B. Notably, rRNA, tRNA, U2 snoRNA, U6 snoRNA, miR812, and miR1122 are significantly enriched in both Class I and Class II superfamilies. miR5565, miR9563, miR6217, miR2593, and miR1435 are enriched solely in Class II TE. Additionally, snR71 is enriched only in the Gypsy superfamily, U1 in PIF-Harbinger , and miR2593 and miR1435 in Mariner . Finally, statistics on miR812 and miR9563 across various genomes, as shown in Fig. 2 C, revealed that the miR812 family is present solely in some monocot species and is particularly abundant in certain Oryza species, where it plays a role in immunity against fungal infections 54 ; In contrast, miR9563 is found exclusively in the Brassicaceae family and is prevalent in certain Brassica species, and is reported to be involved in sugar metabolism, lipid metabolism, and pollen tube growth 55 . Overall, our analysis supports that TEs function as genetic tools leading to lineage speciation through the birth of lineage-specific RNAs 56 , 57 , which exhibit strong family-specific characteristics, but the roles of most ncRNAs originating from TEs remain to be revealed. Genes Domesticated from TEs TEs contribute to host genome evolution as a rich source of novel genes arising from domestication of TE-encoded genes. In Arabidopsis , TE sequences are associated with 7.8% of expressed genes, with 1.2% potentially contributing to protein-coding regions 20 . There are likely many additional genes that have escaped detection due to sequence divergence, obscuring their similarity to transposases 58 , 59 . Moreover, in most cases, the function of these genes remains unknown, raising the question of whether each gene has acquired a distinct role or if there are shared functions among them. To address this, we conducted statistical and enrichment analyses on genes domesticated from TEs. In contrast to ncRNAs, as shown in Fig. 2 D, over three-quarters of the genes domesticated from TEs overlap with class I TEs, with the Copia family being the most prevalent, accounting for 44%. Using all TE-overlapping genes as a background, we subsequently performed a functional enrichment analysis for genes related to each TE superfamily. The top ten significantly enriched functional gene families were mapped to their corresponding TE superfamilies to create a network, as shown in Fig. 2 E. Terms such as ‘nucleic acid,’ ‘binding DNA integration,’ ‘zinc ion binding,’ ‘DNA binding,’ ‘ATP binding,’ ‘RNA-DNA hybrid ribonuclease activity,’ and ‘protein binding’ were significantly enriched in both Class I and class II superfamilies, while ‘DNA helicase,’ ‘DNA repair,’ ‘sequence-specific DNA binding,’ ‘telomere maintenance,’ and ‘DNA-mediated transposition’ were enriched in class II TE superfamilies. Finally, statistics on DNA repair genes in various genomes indicate that, as shown in Fig. 2 F, these genes are abundant in most higher plants and particularly rich in certain angiosperms (such as the Arachis genus ). In summary, class I TE superfamilies transposase genes are the primary source of TE-origin genes, and the functional genes derived from each TE superfamily exhibit strong family-specific characteristics. Gene Duplications Induced by TEs In the context of adaptation, the expansion of gene families can lead to the functional diversification of genes, which is crucial for adapting to new environments 60 – 64 . TEs are major drivers of gene family expansion. Here, integrating the similarity information of genes and upstream/downstream TEs, we identified 10,488,967 TE-induced gene duplications, accounting for 40.83% of the total genes. Our statistics indicate that, as shown in Fig. 2 G, over 80% of the duplicated genes were induced by Class II TEs, with Helitron being the most prevalent, accounting for 21%, followed by Mutator . Many TEs cluster into TE islands, which supports the idea that functional genomic regions are frequently revisited by TEs 48 . Using all TE-induced duplication genes as a background, we subsequently performed a functional enrichment analysis for genes related to each TE superfamily. Figure 2 H shows the top 20 significantly enriched functional gene families, and biosynthetic function genes were significantly enriched in both the class I and class II superfamilies, with the total proportion of each TE family exceeding 100%, suggesting that different TE families might collaborate in the gene duplication process. ‘Phototropism’ was enriched in class I Gypsy , and ‘meristem maintenance’ is significantly enriched in both Helitron and Mutator , a phenomenon also observed in recently active TEs. ‘Double-strand break repair’ was significantly enriched in both Helitron and CACTA, indicating that these gene families may participate in the transposition process of these TEs. Finally, statistics on meristem development genes in various genomes indicate that, as shown in Fig. 2 I, these genes are abundant in most higher plants and particularly rich in some angiosperms (such as Urochloa decumbens ). Transposed duplications are prevalent among disease resistance gene homologs 32 , indicating that there may be nonrandom, recurrent patterns in the origin of gene family members across diverse evolutionary lineages. Ther has been more than one burst for each TE family over several million years 65 . When a TE captures a functional gene and subsequently bursts, it can facilitate the expansion of the functional gene family (Fig. 1 D). Here, by comparing gene family expansion across different lineages, we identified 1,097 bursts (genes of a family duplicated over 100 times) involving 114 species (Table S6 ) . Among these, Oryza sativa presented the greatest number of bursts, occurring 24 times, followed by Brassica oleracea with 20 bursts. In terms of TE superfamily comparisons, Helitron was the most common, with 396 bursts, followed by Gypsy with 311 bursts. The gene families involved mainly include those related to ATP synthase and metabolism, meristem development, phototropism, and telomere maintenance, among others. Understanding the Roles of TEs in Plant Evolution In plants, compact series of rather recent speciation events are typically exemplified by pangenome sequencing projects 40–43,66−71 . However, it is not well known when and how these species have diversified; therefore, this topic has been an issue of profound interest that has yet to be resolved. According to Darwin’s perspective, evolution can be restated as a process in which genomes generate genetic innovations, which are then selected by the environment and incorporated into the genome, ultimately leading to the emergence of new species 6 , 7 . This can be further broken down into two key questions: What unique functional innovations are found in different plant lineages? How are these functions acquired? To address the first question, As shown in Fig. 3 A, we begin by grouping plant species according to their evolutionary lineages and then constructing a 558 × 72,537 matrix on the basis of the number of functional genes/ncRNAs in each genome. Through supervised machine learning classification, we assess the importance of each functional family. Combined with statistical tests of interpopulation differences, this approach allows us to identify functional features specific to each plant group. Thus, by conducting cross-species comparisons and analyzing functional genes significantly influenced by TEs, we can partially address the second question. Revealing the Contribution of TEs to Angiosperm Evolution To identify characteristic functional gene families of angiosperms, we first classified 352 species into five groups on the basis of evolutionary lineage: algae, mosses, ferns, gymnosperms, and angiosperms. Next, we compared the angiosperm group with the other four groups in pairs, and used a random forest machine learning classifier to select the characteristic functional families of angiosperms. We then used Student's t test to assess the significance of differences in each characteristic among the groups Fig. 3 A and Table S7 . Finally, we identified 22 TE-associated functional gene families and 5 TE-associated ncRNA families. Figure 3 B shows the average gene numbers of these gene families in each group, indicating that 8 of these functional gene families are exclusive to angiosperms, such as cyclin D6, whereas other functional gene families have significantly greater member numbers in angiosperms than in the other groups. Furthermore, we selected three functional gene families. By analyzing TE-mediated gene duplications and the proportion of TE-origin genes (Fig. 3 C), we found that TEs primarily mediate gene duplication in the Cyclin D6 functional gene family. In contrast, TEs may provide functional elements and mediate gene duplication in the genetic innovations of the FAR1, zinc finger SWIM3, and MYB transcription factor gene families (Fig. 4 ), all of which are specific to the angiosperm lineage (Fig. 4 B). FAR1 genes are domesticated from Mutator-like transposases (MULEs), research on Arabidopsis reported they regulate phytochrome A signaling 37 , 72 , 73 . We also found that the zinc finger SWIM3 transcription factors derived from Mutator, and MYB transcription factors derived from CACTA transposase, have undergone significant expansion in angiosperms 74 , which control chloroplast biogenesis 75 ( Fig. 4 C ) . Next, we further analyzed the functional gene family characteristics of monocots and dicots via this functional family screening process, with relevant results shown in ( Table S7 , Fig. 5 and Fig S3 ). In dicots, a horizontal comparison across seven families, as shown in Fig. 5 , revealed that enzymes are the most prevalent among the family-specific functional genes, accounting for 52.34%, and transcription factors accounting for 8.77%. In monocots, as shown in Fig S3 , various enzymes accounting for 47.5% and transcription factors accounting for 9.17%, Vertical analysis of four key evolutionary nodes in rice revealed that the evolution from monocots to the family Poaceae and then to the subfamily Oryza was associated with the development of new gene functions. In the final stage of cultivated rice, the top 10 functional genes are related to an increase in quantity. Overall, this study identified 1563 gene family characteristics unique to different lineages of angiosperms, with various enzymes accounting for 49.52% and transcription factors accounting for 9.08%, which allows us to trace the contribution of TEs to genetic functional innovation across various stages and branches of plant evolution. Comprehending Routes of Synthase Evolution TE-free genes are involved in critical functions such as development, transcription, and the regulation of transcription, whereas TE-rich genes are involved in functions such as transport and metabolism, which could be explained by a stronger selection pressure acting on both the coding and noncoding regions of TE-free genes than on those of TE-rich genes 76 . In line with this observation, various enzymes make up nearly half of the TE-associated gene families, with synthases being the most prevalent, with 16 out of 18 being terpenoid synthases, which play roles in defense and growth regulation. To gain a deeper understanding of the impact of TEs on synthase gene families, we conducted a comprehensive analysis of 18 synthase gene families, that were lineage specific ( Fig. 6 A). The first 9 gene families are specific to dicot lineages, whereas the remaining 9 are specific to monocot lineages. Notably, K14037 ent-sandaracopimaradiene/labdatriene synthase is specific to the monocot lineage ( Oryzoideae ), yet in a dicot (Heracleum sosnowskyi), there are up to 100 genes in this family. Moreover, K14037-related proteins have not been annotated in Daucus carota or other dicots within Apiaceae , suggesting that this protein family in Heracleum sosnowskyi may have originated from TE-mediated horizontal gene transfer ( Fig. 6 B ) , moreover, TE annotation of gene regions shows that the expansion of this gene family is TE-mediated ( Fig. 6 C ). Notably, class I Copia -induced duplication genes have only 1 exon, whereas class II Mutator -induced duplication genes have 3 exons ( Fig S4 ), which aligns with stress-responsive genes located near the TE families tend to be substantially shorter in length with fewer introns 77 . Discussion In this study, we propose a machine learning-based framework to identify key genetic innovation events associated with TEs. We performed a comprehensive identification of TEs across 558 genomes on the basis of integrated functional genomic annotations, resulting in a large dataset of TE-associated genetic innovation events across 352 species. This includes the generation of new functional genes by domesticated transposases, the production of ncRNAs, and TE-mediated gene duplications and gene family expansions, which are significantly enriched in 2,805 functional terms. We then grouped the genomes according to their genetic lineages, combining feature selection through machine learning and population difference analysis to identify lineage-specific functional features. Finally, we integrated lineage-specific genetic factors with TE-related genetic innovations to determine the contributions of TEs to lineage-specific genetic functional innovations and infer the role of TEs in plant functional genomic evolution. We conclude that enzymes (e.g., synthases) and chromatin-related factors (e.g., transcription factors) exhibit functional innovations with TEs playing a significant role in plant evolution. Our study and results validated and refined McClintock’s observations and hypotheses 33 through large-scale comparative studies across species, providing a new method for research on TEs in the context of plant evolution. Angiosperms, the most diverse group of flowering plants, exhibit a wide range of functional characteristics that reflect their adaptations to various environmental conditions and growth scenarios. This study systematically analyzes the lineage-specific functional genes of two angiosperm classes (dicots and monocots) across eight families and examines the role of TEs in the evolution of these functional genes. Our results revealed that during the early stages of evolution, TE-associated genetic innovations were observed in cyclin D6 and transcription factors, such as FAR1 genes, which regulate phytochrome A signaling and are derived from Mutator-like transposases (MULEs) 37 , 72 , 73 . In later stages, functional innovations became prominent in enzyme-encoding gene families, particularly in various synthetases, which is reflected in the diverse functional properties of secondary metabolites in plants. This fundamental genomic understanding is likely to be valuable for crop improvement. Oliver et al. documented 65 examples of TE insertions in regulatory or coding sequences that affect a wide range of phenotypic traits, such as skin color in grapes 78 and anthocyanin accumulation in blood oranges 79 , highlighting the importance of genome-wide neofunctionalization in generating new variations 80 . Analysis of lineage-specific functional genes at different evolutionary stages in Oryzoideae suggests that TE-associated miRNAs may have played a role in the evolution of this group, indicating that the evolution and selection of small RNAs are potentially important processes in crop plants, including rice 81 , 82 and corn 80 . In addition to known cases where TE insertions or duplicated genes affect plant traits, the broader significance of these events is increasingly recognized, even when the specific mechanisms are not fully understood. Further research is needed to harness this biological knowledge to enhance traits of agronomic importance. Owing to their inherent ability to carry and integrate DNA into foreign genomes, transposable elements (TEs) are widely used tools in genetic engineering 83 . To optimize TE-based genetic tools and design effective strategies, it is essential to systematically understand the roles of TEs as “nature’s genetic engineers”. This study systematically assessed the roles and patterns of TEs in functional genomic innovations in plants, identifying 1,258,230 genes originating from TEs, 1,165,059 ncRNAs derived from TEs, and 10,488,967 TE-induced gene duplications (Table S2 ) . This resource is particularly valuable for those interested in understanding the factors underlying transposition activity and evolutionary dynamics, as well as for expanding the TE toolbox. Our results indicate that TE-induced gene duplications, followed by mutations and natural selection, predominantly generate new functions. Analysis of lineage-specific functional genes affected by TEs revealed that transcription factors and synthetases are the most impacted categories. Specifically, an analysis of TE-associated synthases revealed that TEs capture certain terpene synthases, mediating gene family expansion within species and potentially facilitating horizontal gene transfer related to K14037 genes. A similar phenomenon has been observed in the horizontal transfer of BtPMaT1 between plants and whiteflies 84 . The extent and dynamics of horizontal gene transfer mediated by TEs between species warrant further investigation. This study contributes significantly to our understanding of how TEs drive plant genome evolution. An analysis of high-quality genomic assemblies from 352 species across five plant phyla, revealed the extensive role of TEs in generating genetic diversity. The comprehensive identification of more than 460 million TEs and their associated transposase domains, along with their impacts on genes and ncRNAs, reveals how TEs contribute to the creation of new genes and gene duplications. This not only enhances our grasp of the evolutionary processes influenced by TEs but also identifies 2,805 functional gene families, with 1563 likely crucial at key evolutionary stages. This study highlights the critical role of TEs as ‘nature’ genetic engineers’ and suggests that understanding TE-driven adaptive evolution can guide improvements in synthetic biology tools and strategies. Insights into the evolutionary pathways of synthetic enzymes, informed by TE dynamics, could lead to advancements in synthetic biology. This set the stage for future research to validate these evolutionary roles, explore their impact in various environmental contexts, and integrate these insights into applications in crop improvement and biotechnology. Continued advancements in sequencing technologies and genomic data analysis will further refine our understanding of TE dynamics and their contributions to plant evolution. Materials and methods Characterization and Annotation of TEs Data collection High-quality genomes provide a direct and reliable avenue for the comprehensive identification of TEs and tracing their proliferation and activity. In pursuit of this objective, we amassed a collection of 558 publicly available reference-quality genomes on the basis of four distinct criteria: 1) they belong to species of significant importance; 2) the assembly level is at least at the chromosome level; and 3) complete functional gene annotations are available. The genomes and their functional gene annotations were downloaded from the databases listed in Table S1 (accessed on June 20, 2024) . We conducted a genome evaluation on the downloaded genomes (Table S1 ). Transposable elements annotation TEs were identified via a method that combines de novo structure analyses and homology from two repeat detection programs Extensive de novo TE Annotator software version 2.0.1 (EDTA) 44 . EDTA incorporates LTRharvest, LTR_FINDER, LTR_retriever, TIR-Learner, HelitronScanner, RepeatModeler, and RepeatMasker, as well as customized filtering scripts for de novo identification of each TE class, and compiles the results into a comprehensive TE library. The RepeatMasker (version 4.0.5) 85 and the final EDTA repeat libraries were subsequently used to soft mask the genome assemblies prior to annotation. Because RepeatMasker reported identity. Young TEs and aged TEs are defined as annotations that are > 95% identical to the intact TE entries, or < 95% identical, respectively. Next, to identify protein or nucleic acid sequence homology to proteins encoded by diverse families of transposable elements, we used homology searching of the 558 genome assembled sequences against curated conserved ORFs of TEs using TransposonPSI ( http://transposonpsi.sourceforge.net/ ) 46 with the parameter ‘nuc’. The best hits were realigned via exonerate, and the proteins with TE copies were extracted. Gene and ncRNA annotation Protein domains were predicted using InterProScan 86 (v.4.8) based on the InterPro (v.32.0) ( http://www.ebi.ac.uk/interpro/ ) database, which also provides a portal for obtaining GO terms ( http://geneontology.org/ http://www.geneontology.org/page/go-database ) 87 . Pathways of the genes were identified via BLAST searches against the Kyoto Encyclopedia of Genes and Genomes (KEGG; https://www.genome.jp/kegg/ ) database 88 . TFs were identified by performing BLASTP searches against the plant transcription factor database PlantTFDB version 5.0 ( http://planttfdb.gao-lab.org/ ) 89 . Flowering time genes were annotated based on FLOR-ID 90 . For noncoding RNA prediction, Infernal 91 (v1.1.5) was used to identify ncRNAs on the basis of the Rfam database 92 . Assessing the impact of TEs on the Host Genome Assessed co-locations or overlapping with other genomic features The genomic TEs and transposase domains were categorized as being in gene regions (overlapping with a functional protein), upstream and downstream regions (within a 2-kb region upstream or downstream from the transcription start site), and ncRNA regions (overlapping with a ncRNA). For each genome assembly, the overlap of TEs with different genomic features was performed using BEDtools 93 , which intersects with the parameter “-f 0.5” and the number of TEs by superfamily (i.e., summing independently for Copia, Gypsy , CACTA, hAT, Mutator , Tc1-Mariner, PIF-Harbinger, Helitron , and other unclassified TEs) was determined. Detection of domesticated transposases and TEs The selection of domesticated transposases and TEs is divided into two steps: Step 1: Identify genes that overlap with transposase domains as candidates for domesticated transposases, and ncRNAs that overlap with TEs as candidates for ncRNAs originating from TEs. Step 2: Count the number of species within 352 species that contain the gene/ncRNA family, as well as the number of species with evidence of domesticated TEs. If the proportion of species with evidence is greater than 50%, they are considered likely to originate from TEs. Detect TE induced gene duplications A modified DupGen_finder pipeline was used to identify gene duplications 94 . Briefly, all-versus-all BLASTP was performed via OrthoFinder to search for potential homologous gene pairs. DupGen_finder was then used to identify whole-genome duplication (WGD), proximal duplication (PD), tandem duplication (TD), transposed duplication (TRD), and dispersed duplication (DSD) gene pairs. For further analysis, we focused only on TRD and DSD genes, as WGD, PD and TD duplicates may not have been caused by TEs. Next, we filtered out gene pairs without TE evidence support (requiring cosine similarity > 0.5 of TE components between the two genes of each gene pair). Finally, for each functional gene family, we counted the number of family genes in each species and the number of TE-mediated duplicated genes. We then assessed the impact of TEs on the expansion of functional gene families by evaluating the correlation between these two factors. Assessing the impact of TEs on genetic functions of plants Gene and ncRNA enrichment analysis To investigate the interplay between TEs and the host genome, we conducted enrichment analyses focusing on genes and ncRNAs associated with TEs. First, for functional genes, enrichment analyses were performed via GO annotations, KEGG annotations, PlantTF annotations, and FLOR annotations. For ncRNAs, enrichment analysis was based on ncRNA families. Second, the choice of background genes varied depending on the analysis objectives. To analyze the impact of each TE superfamily on genetic features, we used all TE-associated genes as the background and performed enrichment analyses for each superfamily-associated gene. To study the effects of TEs on plant evolution, we used all functional genes as the background and conducted enrichment analyses for TE-associated genes. The Python package GSEApy 95 was used for enrichment analysis, with a P value less than 0.01 indicating significant enrichment. Machine Learning for Identifying Plant Lineage-Specific Functional Features The process of selecting lineage-specific functional gene features consists of four main steps: Step 1. The number of genes in each functional gene family for 558 genomes was counted, creating a 558 × 72,537 matrix. Step 2. All genomes were grouped according to their evolutionary lineage, for example, all species were divided into algae, mosses, ferns, gymnosperms, and angiosperms. Step 3. The matrix and grouping data were fed into a random forest model as training data and the importance of each feature as output. Step 4. Furthermoer, Student's t-test was used to assess the significance of differences for each feature among the groups, retaining features with importance > 0 that were significantly different across all groups. Phylogenetic analysis The taxonomic information was retrieved from the NCBI page of each genome, with manual determination for those taxa not found in NCBI page. The phylogenetic cladogram was reconstructed based on the taxonomical NCBI level of all genomes surveyed in this analysis using the NCBITaxa in the Python Environment for Tree Exploration3 (ETE3) v3.1.12 program 96 . iTOL 97 was used to visualize the phylogenetic tree. Declarations Acknowledgements Not applicable. Authors' contributions LX and HY conceived and designed the study. HY performed computational analyses with the help of LX. HY analyzed and interpreted the genome data regarding the evolution of TEs and their host genomes. HY, SSK, SCC, SS and LX were all contributors in writing the manuscript. All authors read and approved the final manuscript. Funding LX is supported by National Key Research and Development Program of China, grant number 2021YFD2200502. The authors have declared that no conflict of interest exists. Availability of data and materials The codes/datasets generated during the current study are available in the Github repository, https://github.com/Color4/TE_Evolution_in_Plants/. Ethics approval and consent to participate Not applicable. Consent for publication Not applicable. Competing interests The authors declare that they have no competing interests. References Bourque, G. et al. Ten things you should know about transposable elements. Genome Biology 19 , doi:10.1186/s13059-018-1577-z (2018). Quesneville, H. Twenty years of transposable element analysis in the Arabidopsis thaliana genome. Mob DNA 11 , 28, doi:10.1186/s13100-020-00223-x (2020). Platt, R. N., Vandewege, M. W. & Ray, D. A. Mammalian transposable elements and their impacts on genome evolution. Chromosome Res 26 , 25-43, doi:10.1007/s10577-017-9570-z (2018). Bennetzen, J. L. & Wang, H. The Contributions of Transposable Elements to the Structure, Function, and Evolution of Plant Genomes. 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TableS1.DataSourceofGenomeAssemblies.xlsx Additional file 2: Table S1 Data Source of Genome Assemblies TableS2.DenovoTEsandTransposasesAnnotationStatistics.xlsx Additional file 3: Table S2 De novo TEs and Transposases Annotation Statistics TableS3.TEassociatedGenesandncRNAsStatistics.xlsx Additional file 4: Table S3 TE-associated Genes and ncRNAs Statistics TableS4.ImpactsofTEsonGeneticFunctions.xlsx Additional file 5: Table S4 Impacts of TEs on Genetic Functions TableS5.ImpactsofTEsSuperfamily.xlsx Additional file 6: Table S5 Impacts of TEs Superfamily TableS6.TEsinducedBurstofGeneFamilies.xlsx Additional file 7: Table S6 TEs induced Burst of Gene Families TableS7.ImpactsofTEsonAngiospermsEvolution.xlsx Additional file 8: Table S7 Impacts of TEs on Angiosperms Evolution TableS8.ImpactsofTEsonPlantSynthaseEnzymes.xlsx Additional file 9: Table S8 Impacts of TEs on Plant Synthase Enzymes TableS9.ExampleofTEInducedGeneDuplications.csv Additional file 10: Table S9 Example of TE Induced Gene Duplications TableS10DataassociatedwithFiguresinthisstudy.xlsx Additional file 11: Table S10 Data associated with Figures in this study GraphicalAbstract.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. 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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-5428092","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":379574578,"identity":"83948401-0853-4026-92d1-e70a694ea748","order_by":0,"name":"Xin Liu","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAwklEQVRIiWNgGAWjYBACPmYgkcBgA+ElEKOFDaIljRQtEOowCQ5jY+cxk3i447xdv3Tz0Q0PauoY+Gc3EHIYj7FB4pnbyTPnHEu7kXDsMIPEnQMEtRg+SGy7nWxwI8fsRmLDAQYDiQSCWgwOJLadS7aHaKkjSgvIlgN2BhJgLczEaGErNkhsS06QuJEG9guPxA0CWvj5D2+T/NlmZ88/I/nYzR81dXL8MwhogYHEBiiDhzj1QGBPtMpRMApGwSgYeQAA49U+Y6RrydkAAAAASUVORK5CYII=","orcid":"","institution":"College of Life Sciences, University of Chinese Academy of Sciences","correspondingAuthor":true,"prefix":"","firstName":"Xin","middleName":"","lastName":"Liu","suffix":""},{"id":379574579,"identity":"b4e8198a-4231-4a74-b07c-96c65a22a066","order_by":1,"name":"Yan Huang","email":"","orcid":"","institution":"College of Life Sciences, University of Chinese Academy of Sciences","correspondingAuthor":false,"prefix":"","firstName":"Yan","middleName":"","lastName":"Huang","suffix":""},{"id":379574580,"identity":"7431364f-a640-41d8-8df8-db8c6d6b9391","order_by":2,"name":"Sunil Sahu","email":"","orcid":"","institution":"BGI Research","correspondingAuthor":false,"prefix":"","firstName":"Sunil","middleName":"","lastName":"Sahu","suffix":""},{"id":379574581,"identity":"758b5ac9-b131-4128-9752-2cf1ec1abd40","order_by":3,"name":"Chengcheng Shi","email":"","orcid":"","institution":"BGI Research","correspondingAuthor":false,"prefix":"","firstName":"Chengcheng","middleName":"","lastName":"Shi","suffix":""},{"id":379574582,"identity":"b80bffa3-d789-4081-a91b-a34b0b6ed188","order_by":4,"name":"Shuai Sun","email":"","orcid":"","institution":"BGI Research","correspondingAuthor":false,"prefix":"","firstName":"Shuai","middleName":"","lastName":"Sun","suffix":""}],"badges":[],"createdAt":"2024-11-11 01:53:22","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-5428092/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-5428092/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":70136431,"identity":"d41a8a9c-1711-4476-b5b8-7ccaeac8f023","added_by":"auto","created_at":"2024-11-28 17:16:00","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":439061,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cem\u003e\u003cstrong\u003eDe novo\u003c/strong\u003e\u003c/em\u003e\u003cstrong\u003e identification of TEs and their impacts. A.\u003c/strong\u003e Pipeline of this study. \u003cstrong\u003eB.\u003c/strong\u003e Young TEs in 352 species. The heatmap shows the young TEs (sequence similarity with intact TEs over 95%) from eight superfamilies (\u003cem\u003eCopia\u003c/em\u003e, \u003cem\u003eGypsy\u003c/em\u003e, hAT, CACTA, PIF-\u003cem\u003eHarbinger\u003c/em\u003e, Mutator, Tc1-\u003cem\u003eMariner\u003c/em\u003e, and \u003cem\u003eHelitron\u003c/em\u003e) from the innermost to the outermost layers. The phylogenetic relationships among the 352 species are based on their lineage. \u003cstrong\u003eC. \u003c/strong\u003ePercentages of three types of genetic innovations in each species. The color of the strip corresponds to species classification, while the bars indicate the percentage of TE associated genes among total genes (orange bars are gene duplications, blue bars indicate genes domesticated from transposases, and purple bars represent ncRNAs originating from TEs). \u003cstrong\u003eD.\u003c/strong\u003e There are two mechanisms through which TEs affect genes: the domestication of new genes and the mediation of gene duplication. Each spot represents a functional gene family, with larger spot sizes indicating more genes. The x-axis shows the correlation between TE-induced duplicated genes and total genes, whereas the y-axis shows the proportion of species containing TE domesticated genes. \u003cstrong\u003eE. \u003c/strong\u003eTop 20 gene families associated with genetic innovations induced by TEs and their median family member counts across six plant populations.\u003c/p\u003e","description":"","filename":"1.png","url":"https://assets-eu.researchsquare.com/files/rs-5428092/v1/3c08adc5a6f7c68df29efb7f.png"},{"id":70136425,"identity":"ef663724-f2cd-4119-9a6c-dbbadcb97634","added_by":"auto","created_at":"2024-11-28 17:15:54","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":434142,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eRole of TE Superfamilies in Genomic Innovation in Plants.\u003c/strong\u003e \u003cstrong\u003eA-C.\u003c/strong\u003e \u003cstrong\u003encRNAs Originating from TEs. \u003c/strong\u003e\u0026nbsp;\u003cstrong\u003eA. \u003c/strong\u003eThe bar plot shows the percentage of ncRNAs derived from eight TE superfamilies in plants. \u003cstrong\u003eB.\u003c/strong\u003e This panel presents a network of the top 10 ncRNA families generated by each TE superfamily, with edge thickness representing the quantity of ncRNAs. Nodes of class I TEs were orange, nodes of class II TEs were pink. \u003cstrong\u003eC. \u003c/strong\u003eThis phylogenetic tree highlights the role of \u003cem\u003eTc1-Mariner\u003c/em\u003e TEs in the proliferation of miR812 in \u003cem\u003ePoaceae\u003c/em\u003eand \u003cem\u003ePIF-Harbinger\u003c/em\u003e TEs in the expansion of miR9563 in \u003cem\u003eBrassicaceae\u003c/em\u003e. \u003cstrong\u003eD-F.\u003c/strong\u003e \u003cstrong\u003eGenes Domesticated from TEs.\u003c/strong\u003e \u003cstrong\u003eD\u003c/strong\u003e depicts the percentage of new genes produced by eight TE superfamilies in plants. \u003cstrong\u003eE\u003c/strong\u003e shows a network of the top 10 gene families generated by each TE superfamily, with edge thickness representing gene quantity. \u003cstrong\u003eF\u003c/strong\u003e demonstrates that \u003cem\u003eHelitron\u003c/em\u003eTEs domesticated to DNA repair genes in most angiosperms. \u003cstrong\u003eG-I.\u003c/strong\u003e \u003cstrong\u003eGene duplications induced by TEs. G\u003c/strong\u003e indicates the percentage of repetitive genes produced by eight TE superfamilies in plants. \u003cstrong\u003eH.\u003c/strong\u003e Heatmap of the top 20 gene families captured and expanded by each TE superfamily, with cell color representing the percentage of repetitive genes within each family. \u003cstrong\u003eI\u003c/strong\u003e The phylogenetic tree shows that \u003cem\u003eMutator\u003c/em\u003e TEs captured and facilitated the expansion of genes related to meristem development in angiosperms.\u003c/p\u003e","description":"","filename":"2.png","url":"https://assets-eu.researchsquare.com/files/rs-5428092/v1/5caf56bc60f4bd87b0aca73f.png"},{"id":70135610,"identity":"311f3b3b-c774-4efe-96c3-aa5d4e507f53","added_by":"auto","created_at":"2024-11-28 17:07:56","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":227969,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eTE induced plant evolution. A.\u003c/strong\u003e Workflow for population trait screening; \u003cstrong\u003eB.\u003c/strong\u003e Top 20 unique functional genes in angiosperms; \u003cstrong\u003eC.\u003c/strong\u003e Three case studies of angiosperm-specific functional genes: (1) Cyclin D6, which was captured and amplified by TEs; (2) zinc finger transcription factors, genes that were domesticated from TEs and subsequently expanded; (3) the FAR1-related sequence, a flowering-related transcription factor that was also domesticated from TEs and expanded by TEs and is unique to angiosperms.\u003c/p\u003e","description":"","filename":"3.png","url":"https://assets-eu.researchsquare.com/files/rs-5428092/v1/6a7681400e81d02ad4172fdb.png"},{"id":70136426,"identity":"d89999fd-b19d-4925-8358-ebcc9d3a7527","added_by":"auto","created_at":"2024-11-28 17:15:54","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":178365,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eDomesticated transposes to transcription factor. A.\u003c/strong\u003e Three transcription factors domesticated from transposases. The scatter plot shows the correlation between TE-associated genes and total genes; the pie chart displays the proportion of species with evidence of domesticated transposases (orange).\u003cstrong\u003e B. \u003c/strong\u003ePhylogenetic tree showing the total number of each gene families in each species and the number of genes associated with TEs (orange bars) in each species. \u003cstrong\u003eC.\u003c/strong\u003e Proportions of transposase superfamilies that overlap with the three transcription factors.\u003c/p\u003e","description":"","filename":"4.png","url":"https://assets-eu.researchsquare.com/files/rs-5428092/v1/9b403e8cf7e85475a0658870.png"},{"id":70135596,"identity":"f1c45734-e31f-4d63-b320-4b42283cfb19","added_by":"auto","created_at":"2024-11-28 17:07:54","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":281152,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eTop 10 functional gene features of the 7 dicot families. A.\u003c/strong\u003e Phylogenetic tree of dicotyledons grouped into 7 families; \u003cstrong\u003eB.\u003c/strong\u003e Functional gene features of 7 dicot families; \u003cstrong\u003eC. \u003c/strong\u003eLineage-specific top 10 functional genes for each of the 7 dicot families. In the figure, the first column, ‘Group’, represents the plant groups from which the characteristic genes originate. The second column shows yellow for the catalytic enzyme gene families, pink for the transcription factor families, and blue for the other families. The third column contains a heatmap showing the average gene counts for corresponding gene families in each family.\u003c/p\u003e","description":"","filename":"5.png","url":"https://assets-eu.researchsquare.com/files/rs-5428092/v1/01e90fe67a313a3e30d3b398.png"},{"id":70136428,"identity":"10e35ac1-eb6e-4942-87fa-ae0aef906a72","added_by":"auto","created_at":"2024-11-28 17:15:54","extension":"png","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":305528,"visible":true,"origin":"","legend":"\u003cp\u003e\u003cstrong\u003eEvolution of Plant Synthase Enzymes. A.\u003c/strong\u003e Synthase enzymes unique to the lineages of monocots and dicots. \u003cstrong\u003eB.\u003c/strong\u003eThe correlation between TE-associated duplication genes and total genes for each lineage-specific synthase family across species. \u003cstrong\u003eC.\u003c/strong\u003e Number of K14037 synthase family genes in the monocot \u003cem\u003eOryzoideae\u003c/em\u003e subfamily and the dicot \u003cem\u003eHeracleum sosnowskyi\u003c/em\u003e. The orange portion represents TE-associated duplication genes.\u003cstrong\u003e D\u003c/strong\u003e. Class I \u003cem\u003eCopia\u003c/em\u003e TEs mediate the expansion of the K14037 synthase gene family in \u003cem\u003eHeracleum sosnowskyi\u003c/em\u003e.\u003c/p\u003e","description":"","filename":"6.png","url":"https://assets-eu.researchsquare.com/files/rs-5428092/v1/7f36ad72aa97bf3f84cfe764.png"},{"id":91889579,"identity":"1c02ec2f-7be0-4009-ae0a-cb8b832a1e11","added_by":"auto","created_at":"2025-09-22 15:55:42","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":2841374,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5428092/v1/a60a6a8b-5ec7-4d94-b3db-a98cfdf186a9.pdf"},{"id":70135595,"identity":"caefb235-a745-4d86-880a-3e25f7edb4fe","added_by":"auto","created_at":"2024-11-28 17:07:53","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":1252718,"visible":true,"origin":"","legend":"\u003cp\u003eAdditional file 1: Supplementary Figures. Contains all \u0026nbsp;\u0026nbsp;supplementary figures and figure legends.\u003c/p\u003e","description":"","filename":"supplementaryfigures.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5428092/v1/ec054e672be037f5448baea7.pdf"},{"id":70135612,"identity":"b1cf5e83-729a-4b25-aeef-9867ae5c75c3","added_by":"auto","created_at":"2024-11-28 17:08:00","extension":"xlsx","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":81913,"visible":true,"origin":"","legend":"\u003cp\u003eAdditional file 2: Table S1 Data Source of Genome \u0026nbsp;\u0026nbsp;Assemblies\u003c/p\u003e","description":"","filename":"TableS1.DataSourceofGenomeAssemblies.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-5428092/v1/5557dbf7176959738f48e244.xlsx"},{"id":70135597,"identity":"603bc430-155b-4162-b24f-9ef57e599461","added_by":"auto","created_at":"2024-11-28 17:07:54","extension":"xlsx","order_by":3,"title":"","display":"","copyAsset":false,"role":"supplement","size":193472,"visible":true,"origin":"","legend":"\u003cp\u003eAdditional file 3: Table S2 De novo TEs and Transposases Annotation \u0026nbsp;\u0026nbsp;Statistics\u003c/p\u003e","description":"","filename":"TableS2.DenovoTEsandTransposasesAnnotationStatistics.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-5428092/v1/a8efa092a0456c927342a78a.xlsx"},{"id":70135609,"identity":"36092015-6e97-473f-bbc3-f77ddabcec8a","added_by":"auto","created_at":"2024-11-28 17:07:55","extension":"xlsx","order_by":4,"title":"","display":"","copyAsset":false,"role":"supplement","size":79131,"visible":true,"origin":"","legend":"\u003cp\u003eAdditional file 4: Table S3 TE-associated Genes and ncRNAs \u0026nbsp;\u0026nbsp;Statistics\u003c/p\u003e","description":"","filename":"TableS3.TEassociatedGenesandncRNAsStatistics.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-5428092/v1/3a99b930ee0414fb054ec5bc.xlsx"},{"id":70135608,"identity":"371e0109-029e-4e0d-bb5b-f8c5a27c88ce","added_by":"auto","created_at":"2024-11-28 17:07:55","extension":"xlsx","order_by":5,"title":"","display":"","copyAsset":false,"role":"supplement","size":19853562,"visible":true,"origin":"","legend":"\u003cp\u003eAdditional file 5: Table S4 Impacts of TEs on Genetic \u0026nbsp;\u0026nbsp;Functions\u003c/p\u003e","description":"","filename":"TableS4.ImpactsofTEsonGeneticFunctions.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-5428092/v1/df313c20b0c6a98d098b906d.xlsx"},{"id":70135607,"identity":"79599dae-6c6c-491a-a6fc-e00ec5186afb","added_by":"auto","created_at":"2024-11-28 17:07:54","extension":"xlsx","order_by":6,"title":"","display":"","copyAsset":false,"role":"supplement","size":26934600,"visible":true,"origin":"","legend":"\u003cp\u003eAdditional file 6: Table S5 Impacts of TEs Superfamily\u003c/p\u003e","description":"","filename":"TableS5.ImpactsofTEsSuperfamily.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-5428092/v1/fc8e79b0a4d9031f23552556.xlsx"},{"id":70136901,"identity":"096fe999-eda0-4b59-9edb-3df154e2466a","added_by":"auto","created_at":"2024-11-28 17:23:54","extension":"xlsx","order_by":7,"title":"","display":"","copyAsset":false,"role":"supplement","size":723097,"visible":true,"origin":"","legend":"\u003cp\u003eAdditional file 7: Table S6 TEs induced Burst of Gene Families\u003c/p\u003e","description":"","filename":"TableS6.TEsinducedBurstofGeneFamilies.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-5428092/v1/bfb3c81264827d171e76d163.xlsx"},{"id":70136427,"identity":"658cac3d-77f8-4720-9561-71571d33cd6b","added_by":"auto","created_at":"2024-11-28 17:15:54","extension":"xlsx","order_by":8,"title":"","display":"","copyAsset":false,"role":"supplement","size":179685,"visible":true,"origin":"","legend":"\u003cp\u003eAdditional file 8: Table S7 Impacts of TEs on Angiosperms \u0026nbsp;\u0026nbsp;Evolution\u003c/p\u003e","description":"","filename":"TableS7.ImpactsofTEsonAngiospermsEvolution.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-5428092/v1/a3d1c15435d98f0aac7b86b3.xlsx"},{"id":70135600,"identity":"c9544cac-2d14-4790-ab4a-377f4e098f43","added_by":"auto","created_at":"2024-11-28 17:07:54","extension":"xlsx","order_by":9,"title":"","display":"","copyAsset":false,"role":"supplement","size":13726,"visible":true,"origin":"","legend":"\u003cp\u003eAdditional file 9: Table S8 Impacts of TEs on Plant \u0026nbsp;\u0026nbsp;Synthase Enzymes\u003c/p\u003e","description":"","filename":"TableS8.ImpactsofTEsonPlantSynthaseEnzymes.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-5428092/v1/6ee725f594a1bf12516d1081.xlsx"},{"id":70137120,"identity":"a8349dc6-8a28-4080-bd2a-95b35478a752","added_by":"auto","created_at":"2024-11-28 17:31:54","extension":"csv","order_by":10,"title":"","display":"","copyAsset":false,"role":"supplement","size":30193,"visible":true,"origin":"","legend":"\u003cp\u003eAdditional file 10: Table S9 Example of TE Induced Gene Duplications\u003c/p\u003e","description":"","filename":"TableS9.ExampleofTEInducedGeneDuplications.csv","url":"https://assets-eu.researchsquare.com/files/rs-5428092/v1/ed7838a50536f5314a4936a2.csv"},{"id":70135602,"identity":"86a72fe6-91e7-47db-8a39-b063dc75dd0a","added_by":"auto","created_at":"2024-11-28 17:07:54","extension":"xlsx","order_by":11,"title":"","display":"","copyAsset":false,"role":"supplement","size":543075,"visible":true,"origin":"","legend":"\u003cp\u003eAdditional file 11: Table S10 Data associated with Figures in \u0026nbsp;\u0026nbsp;this study\u003c/p\u003e","description":"","filename":"TableS10DataassociatedwithFiguresinthisstudy.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-5428092/v1/be8d087e8aaac347e790519b.xlsx"},{"id":70135606,"identity":"b0fd0051-f741-4cee-9806-c4caf2b9418e","added_by":"auto","created_at":"2024-11-28 17:07:54","extension":"pdf","order_by":12,"title":"","display":"","copyAsset":false,"role":"supplement","size":2071538,"visible":true,"origin":"","legend":"","description":"","filename":"GraphicalAbstract.pdf","url":"https://assets-eu.researchsquare.com/files/rs-5428092/v1/2e3523731206418ec031353e.pdf"}],"financialInterests":"No competing interests reported.","formattedTitle":"Machine learning based pan-plant analyses of transposable elements across 352 species illuminates genome evolution","fulltext":[{"header":"Background","content":"\u003cp\u003eTransposable elements (TEs) are DNA fragments that can move and amplify within the genome, and are believed to constitute one major type of \u0026ldquo;nature\u0026rsquo;s genetic engineer\u0026rdquo; in evolution\u003csup\u003e\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e,\u003cspan citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e\u003c/sup\u003e. They play a key role in genome function, speciation, and diversity\u003csup\u003e\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e,\u003cspan citationid=\"CR4\" class=\"CitationRef\"\u003e4\u003c/span\u003e\u003c/sup\u003e, shaping both individual genes and the entire genome. TEs were first discovered in the 1940s by Barbara McClintock\u003csup\u003e\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e\u003c/sup\u003e. Since then, numerous types of TEs have been identified in the genomes of both plants and animals\u003csup\u003e\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e\u003c/sup\u003e. TEs serve as an extraordinary source of evolutionary novelties and have been involved in the evolution of several important biological processes across eukaryotes \u003csup\u003e\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e,\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e\u003c/sup\u003e. As significant players in genome evolution, TEs can be activated under stress conditions, introducing novel structural variation in the insertion sites, which can lead to the generation of new genes and the modification of existing gene structures through the duplication, mobilization and recombination of gene fragments\u003csup\u003e\u003cspan additionalcitationids=\"CR9\" citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e\u003c/sup\u003e. During the evolution of plants from lower to higher taxa, the functional diversity of genes markedly increased. However, the specific roles and impacts of TEs in this process\u0026mdash;specifically how and where they exert their influence\u0026mdash;remain largely unclear.\u003c/p\u003e \u003cp\u003eTEs may act as reservoirs for generating new gene variants through recombination\u003csup\u003e\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e\u003c/sup\u003e, and they can also facilitate cellular functions by sharing transposase-coding regions\u003csup\u003e\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e\u003c/sup\u003e. By inserting themselves into protein-coding genes, TEs can affect genes\u003csup\u003e\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e\u003c/sup\u003e either by providing novel regulatory sequences\u003csup\u003e\u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e\u003c/sup\u003e or by mutating the interrupted gene\u003csup\u003e\u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e\u003c/sup\u003e. This process is known as \u0026lsquo;molecular domestication\u0026rsquo; \u003csup\u003e\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e\u003c/sup\u003e, in which transposase genes acquire mutations so that their products (transposases, reverse transcriptases, integrases, coat proteins, etc.) no longer function in catalyzing transposition and instead evolve novel functions. Domesticated transposases have been identified from both forward genetic screens on the basis of phenotypes, and bioinformatic analyses of genome sequences \u003csup\u003e\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e\u003c/sup\u003e. TE domestication has been reported in both animals and plants. In the human genome, at least 50 genes have been domesticated from TEs\u003csup\u003e\u003cspan additionalcitationids=\"CR18\" citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e\u003c/sup\u003e. In \u003cem\u003eArabidopsis thaliana\u003c/em\u003e, 7.8% of expressed genes contained sequences from TEs, whereas 1.2% had translation evidence suggesting the exonization of TEs\u003csup\u003e\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e\u003c/sup\u003e. Beyond the exaptation of the entire transposase, computational analyses have demonstrated that partial TE sequences have been incorporated into protein-coding genes. Chimeric transcripts between TEs and protein coding genes tend to be common \u003csup\u003e\u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e,\u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e\u003c/sup\u003e. Similarly, Class I Alu TEs in human are present in \u0026sim;10% of mature mRNAs\u003csup\u003e\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e\u003c/sup\u003e. Additionally, growing evidence indicates a close association of TEs with non-coding RNAs (ncRNAs), with a significant number of small ncRNAs originating from TEs \u003csup\u003e\u003cspan additionalcitationids=\"CR25\" citationid=\"CR24\" class=\"CitationRef\"\u003e24\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e\u003c/sup\u003e. The presence of domesticated TEs suggests that TEs may play an active role in gene evolution. However, larger-scale analyses are needed to better understand their specific contributions.\u003c/p\u003e \u003cp\u003eTEs can sequester host genes, inducing their duplication and vertical transfer to descendants. Transposed duplication (TRD) generates a gene pair comprising of an ancestral locus and a novel locus, and is presumed to arise from distantly transposed duplication that occur via DNA-based or RNA-based mechanisms\u003csup\u003e\u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e,\u003cspan citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e\u003c/sup\u003e. DNA transposons, such as packmules (rice)\u003csup\u003e\u003cspan citationid=\"CR29\" class=\"CitationRef\"\u003e29\u003c/span\u003e\u003c/sup\u003e, \u003cem\u003eHelitrons\u003c/em\u003e (maize)\u003csup\u003e\u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e\u003c/sup\u003e, and CACTA elements (sorghum)\u003csup\u003e\u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e\u003c/sup\u003e, may relocate duplicated genes or gene segments to new chromosomal positions. RNA-based transposed duplication, often referred to as retrotransposition, typically creates a single-exon retrocopy from a multiexon parental gene by reverse transcription of a spliced messenger RNA. The expansion of gene families can often be attributed to specific modes of gene duplication\u003csup\u003e\u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e32\u003c/span\u003e\u003c/sup\u003e. For instance, DNA-based transposed duplications are prevalent among disease resistance gene homologs, indicating that there may be non-random, recurrent patterns in the origins of gene family members across diverse evolutionary lineages. These observations underscore the need for further investigation into this phenomenon. Moreover, identifying distantly transposed gene duplication at the genomic scale remains a challenging task. Currently, the classification of transposed duplication genes relies primarily on measuring the physical distance and exon count between duplicate genes\u003csup\u003e\u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e\u003c/sup\u003e. However, this approach does not fully utilize the positional and sequence information provided by TEs. Therefore, comprehensive comparative genomics analyses are needed, encompassing both genes and TEs within and across species.\u003c/p\u003e \u003cp\u003eThe advancement of precise and cost-effective sequencing technologies, along with the practice of open data sharing, has led to a remarkable increase in accessible plant genome assemblies over the past decade. Currently, within the NCBI genome database, there exist 2,045 genome assemblies for plants at the chromosome-level or complete level, encompassing 517 genera and 945 species (accessed on June 20, 2024). The initial discovery of TEs was driven by their impact on phenotypes and their widespread presence in the maize genome\u003csup\u003e\u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e\u003c/sup\u003e. Whole-genome sequencing reveals the involvement of TEs at the genomic structure level, providing insights into the functional degree of these TE sequences\u003csup\u003e\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e\u003c/sup\u003e. Although TEs play a significant role in shaping genomic structure and influencing phenotypic variation, much re\u003csup\u003e\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e\u003c/sup\u003emains to be understood about those TEs that have undergone positive selection throughout the evolutionary history of plants. Extensive comparative genomic studies are beginning to shed light on the impact of TEs on plant evolution, including their contributions to genome architecture and their effects on gene expression and phenotypic diversity.\u003c/p\u003e \u003cp\u003eThe idea that genomes are constructed in a Lego-like manner from codons specifying protein domains dates back to McClintock\u0026rsquo;s observations. She noted that developmental patterns in maize varied due to the insertion and excision of chromosome segments, which she referred to as \u0026ldquo;controlling elements\u0026rdquo; \u003csup\u003e\u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e\u003c/sup\u003e. The concept of exon shuffling as the source of diverse protein structures is another variation of this theme\u003csup\u003e\u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e,\u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e36\u003c/span\u003e\u003c/sup\u003e. However, the impact of TEs on genomic genetic innovation has primarily been identified from forward genetic screens based on phenotypes, such as in \u003cem\u003eArabidopsis thaliana\u003c/em\u003e \u003csup\u003e\u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e\u003c/sup\u003e, maize\u003csup\u003e\u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e\u003c/sup\u003e, orange\u003csup\u003e\u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e\u003c/sup\u003e, peas\u003csup\u003e\u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e39\u003c/span\u003e\u003c/sup\u003e and grape. Today, with the advent of large-scale sequencing projects and advancements in sequencing technology, the whole-genome assemblies of an increasing number of species have been published\u003csup\u003e\u003cspan additionalcitationids=\"CR41 CR42\" citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e43\u003c/span\u003e\u003c/sup\u003e. McClintock\u0026rsquo;s observations and hypotheses can be validated and refined through extensive comparative studies across species to systematically assessing the impact of TEs on functional genomics during plant evolution. In this study, we conducted pan-plant comparisons across 558 plant genomes, encompassing 352 species from 221 genera. We meticulously identified all TEs, traced their proliferation and dispersion in plant genomes, and assessed their overlap with other annotated genomic features to identify novel TE-associated genes and ncRNAs. Furthermore, through interspecies comparisons and functional analysis, we can evaluate the specific effects that TEs might have at different evolutionary stages, as well as how these effects emerge. Ultimately, this research aims to illuminate not only the current understanding but also the future potential of evolutionary processes.\u003c/p\u003e"},{"header":"Results","content":"\u003cp\u003eTo comprehensively analyze the composition of transposable elements (TEs) across the plant kingdom and their impact on plant genomes, this study conducted a taxonomically focused survey of assembled genomes from public databases, including NCBI, Ensembl, CNCB, and Phytozome, along with relevant literature. We selected 558 high-quality genomes from 352 species for analysis, representing a broad spectrum of major plant groups, including algae, mosses, ferns, gymnosperms, and angiosperms \u003cb\u003e(Table \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003e)\u003c/b\u003e. The project is divided into three main parts \u003cb\u003e(\u003c/b\u003eFig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eA, \u003cb\u003eFig \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003eA)\u003c/b\u003e: First, TE \u003cem\u003ede novo\u003c/em\u003e annotation was performed on the 558 assembled genomes from 352 species, and the effects of TEs on genome structure and function were analyzed; Second, we examined the role of eight TE superfamilies in driving genetic innovation within plant genomes; Third, we investigated the impact of TEs on plant evolution.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cdiv id=\"Sec3\" class=\"Section2\"\u003e \u003ch2\u003eEffects of TEs on Plant Genomes\u003c/h2\u003e \u003cp\u003e \u003cem\u003eDe novo\u003c/em\u003e identification of TEs\u003c/p\u003e \u003cp\u003eBy employing EDTA\u003csup\u003e\u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e44\u003c/span\u003e\u003c/sup\u003e for \u003cem\u003ede novo\u003c/em\u003e annotation of transposons across 532 genomes from 352 species, and utilizing EDTA annotations from 26 maize genomes downloaded from MaGDB\u003csup\u003e\u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e43\u003c/span\u003e\u003c/sup\u003e, this study analyzed a total of 539.50 Gb of genomic sequences. Among these, 330.90 Gb were identified as TE sequences (constituting 61.33%), and encompassing 461,915,455 transposons, including 256,444,665 (55.52%) Class I transposons (including Copia and Gypsy) and 201,301,619 (43.58%) class II transposons (including hAT, CACTA, \u003cem\u003ePIF-Harbinger\u003c/em\u003e, Mutator, \u003cem\u003eTc1-Mariner\u003c/em\u003e, and \u003cem\u003eHelitron\u003c/em\u003e) (\u003cb\u003eTable \u003cspan refid=\"MOESM2\" class=\"InternalRef\"\u003eS2\u003c/span\u003e\u003c/b\u003e, Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eB\u003cb\u003e)\u003c/b\u003e. The proportion of transposons aligns with previous findings\u003csup\u003e\u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e45\u003c/span\u003e\u003c/sup\u003e, with a greater representation of class I transposon sequences, reflecting their contribution to genome size \u003cb\u003e(Fig \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003eB, Fig \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003eC)\u003c/b\u003e. Furthermore, we annotated conserved domains associated with transposases via TransposonPSI \u003csup\u003e\u003cspan citationid=\"CR46\" class=\"CitationRef\"\u003e46\u003c/span\u003e\u003c/sup\u003e, identifying 67,851,836 transposon domains, which include 61,807,023 (91.09%) class I transposon domains and 6,044,813 (8.91%) class II transposon domains. The number of conserved domains for class II transposons is less than one-tenth that of class I transposons, indicating that class II transposons contain a greater proportion of nonautonomous elements than class I transposons do.\u003c/p\u003e \u003cp\u003eTE-associated Genetic Components\u003c/p\u003e \u003cp\u003eTE insertions can be neutral or even advantageous for the host, leading to long-term retention of TEs in the host genome. This phenomenon referred to as TE exaptation or TE domestication, is a process in which TEs become part of the regulatory and/or coding region of host genes and contribute to diverse phenotypes and important functions\u003csup\u003e\u003cspan citationid=\"CR47\" class=\"CitationRef\"\u003e47\u003c/span\u003e\u003c/sup\u003e. The spatial relationships between TEs and genes provide important evidence of how TEs shape gene evolution and drive genetic innovation. In this study, we systematically identified TEs and other genetic components (functional genes and ncRNAs) within genomes to analyze their sequence colocalization relationships \u003cb\u003e(\u003c/b\u003eFig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eA\u003cb\u003e)\u003c/b\u003e, evaluating TE-associated genetic components across 352 plant species. This analysis led to the identification of 1,258,230 domesticated transposases (accounting for 4.90% of the total genes), 10,488,967 TE-induced gene duplications (accounting for 40.83% of the total genes), and 1,165,059 ncRNAs derived from TEs (accounting for 29.13% of the total ncRNAs) \u003cb\u003e(Table \u003cspan refid=\"MOESM3\" class=\"InternalRef\"\u003eS3\u003c/span\u003e).\u003c/b\u003e Figure\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eC illustrates three types of genetic innovations generated by TEs. Overall, TEs affected about half of the function genes and one-third of the ncRNAs, with TE-induced gene duplications constituting the largest proportion. Domesticated transposase-derived genes are more prevalent in ferns and gymnosperms, whereas their proportion is notably low in algae, while TE-associated ncRNAs are more abundant in monocots.\u003c/p\u003e \u003cp\u003eTE- associated Genetic Function Innovation\u003c/p\u003e \u003cp\u003eTo further determine the impact of TEs on plant genome function, we performed cross-species comparisons and enrichment analyses of the identified TE-associated genetic components. Given that TE-associated genetic components are subject to natural selection and are vertically transmitted along evolutionary lineages\u003csup\u003e\u003cspan citationid=\"CR48\" class=\"CitationRef\"\u003e48\u003c/span\u003e\u003c/sup\u003e, three key characteristics emerged from our comparisons: First, if a gene family is associated with TEs and vertically transmitted, it will be significantly enriched among TE-associated genes. Second, if a gene family is derived from domesticated transposases or TE sequences, it will spread through lineages as plants evolve. Finally, if a gene family is amplified through transposition, the number of family members in different species should be highly correlated with the number of TE-induced family members duplications.\u003c/p\u003e \u003cp\u003eHere, we conducted an enrichment analysis for each genetic function family, assessed the proportion of domesticated sources across all species and calculated the correlation between the total gene count and TE-mediated duplication genes \u003cb\u003e(Table \u003cspan refid=\"MOESM4\" class=\"InternalRef\"\u003eS4\u003c/span\u003e)\u003c/b\u003e. As shown in Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eD, the gene functional families significantly associated with TEs are clustered in the upper right corner of the scatter plot, with many family genes, indicating a synergistic effect of TEs on these functional genes. Additionally, we calculated the median gene counts of the top 20 enriched gene families for TE-associated genetic functional innovations across different plant populations, as shown in Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eE. As expected, most of these functional genes are related to chromatin, such as \"nucleic acid binding, RNA-DNA hybrid ribonuclease, DNA integration, telomere maintenance, DNA helicase activity\", etc. Overall, TEs can influence functional gene families through two dimensions: providing new domains and mediating duplication, with a synergistic effect between the two.\u003c/p\u003e \u003c/div\u003e\n\u003ch3\u003eImpact of TE Superfamilies\u003c/h3\u003e\n\u003cp\u003eThe composition and transposition mechanisms of different TE superfamilies vary\u003csup\u003e\u003cspan citationid=\"CR49\" class=\"CitationRef\"\u003e49\u003c/span\u003e\u003c/sup\u003e, as do their host genome preferences\u003cb\u003e(Fig \u003cspan refid=\"MOESM2\" class=\"InternalRef\"\u003eS2\u003c/span\u003e)\u003c/b\u003e, which may lead to differences in the genetic innovations they mediate. To explore the potential roles of various TE superfamilies in evolutionary processes, we conducted additional statistical and enrichment analyses on TE-associated genetic components for each TE superfamily \u003cb\u003e(Table \u003cspan refid=\"MOESM5\" class=\"InternalRef\"\u003eS5\u003c/span\u003e)\u003c/b\u003e.\u003c/p\u003e \u003cp\u003encRNAs Originating from TEs\u003c/p\u003e \u003cp\u003eThe emergence of ncRNAs from TEs is a crucial adaptive mechanism for plants survival. Research indicates that several ncRNAs are encoded by TEs or by endogenous genes that are likely derived from TEs\u003csup\u003e\u003cspan additionalcitationids=\"CR51\" citationid=\"CR50\" class=\"CitationRef\"\u003e50\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR52\" class=\"CitationRef\"\u003e52\u003c/span\u003e\u003c/sup\u003e. Additionally, ncRNAs encoded by TEs can repress the proliferation of their originating TEs through sequence complementarity (i.e., TE silencing) \u003csup\u003e\u003cspan citationid=\"CR52\" class=\"CitationRef\"\u003e52\u003c/span\u003e,\u003cspan citationid=\"CR53\" class=\"CitationRef\"\u003e53\u003c/span\u003e\u003c/sup\u003e. To analyze the relationship between TEs and host ncRNAs, we conducted statistical and enrichment analyses on TE-origin ncRNAs. As shown in Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eA, Class II DNA accounts for more than 80% of TE-associated ncRNAs, with the \u003cem\u003eTc1-Mariner\u003c/em\u003e family being the most prevalent, accounting for approximately one-third of this total. We then performed a family enrichment analysis for ncRNAs related to each TE superfamily, using all TE-associated ncRNAs as a background. The top 10 significantly enriched ncRNA families were mapped to their corresponding TE superfamilies to create a network, as depicted in Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eB. Notably, rRNA, tRNA, U2 snoRNA, U6 snoRNA, miR812, and miR1122 are significantly enriched in both Class I and Class II superfamilies. miR5565, miR9563, miR6217, miR2593, and miR1435 are enriched solely in Class II TE. Additionally, snR71 is enriched only in the \u003cem\u003eGypsy\u003c/em\u003e superfamily, U1 in \u003cem\u003ePIF-Harbinger\u003c/em\u003e, and miR2593 and miR1435 in \u003cem\u003eMariner\u003c/em\u003e. Finally, statistics on miR812 and miR9563 across various genomes, as shown in Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eC, revealed that the miR812 family is present solely in some monocot species and is particularly abundant in certain \u003cem\u003eOryza\u003c/em\u003e species, where it plays a role in immunity against fungal infections\u003csup\u003e\u003cspan citationid=\"CR54\" class=\"CitationRef\"\u003e54\u003c/span\u003e\u003c/sup\u003e; In contrast, miR9563 is found exclusively in the \u003cem\u003eBrassicaceae\u003c/em\u003e family and is prevalent in certain \u003cem\u003eBrassica\u003c/em\u003e species, and is reported to be involved in sugar metabolism, lipid metabolism, and pollen tube growth\u003csup\u003e\u003cspan citationid=\"CR55\" class=\"CitationRef\"\u003e55\u003c/span\u003e\u003c/sup\u003e. Overall, our analysis supports that TEs function as genetic tools leading to lineage speciation through the birth of lineage-specific RNAs\u003csup\u003e\u003cspan citationid=\"CR56\" class=\"CitationRef\"\u003e56\u003c/span\u003e,\u003cspan citationid=\"CR57\" class=\"CitationRef\"\u003e57\u003c/span\u003e\u003c/sup\u003e, which exhibit strong family-specific characteristics, but the roles of most ncRNAs originating from TEs remain to be revealed.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eGenes Domesticated from TEs\u003c/p\u003e \u003cp\u003eTEs contribute to host genome evolution as a rich source of novel genes arising from domestication of TE-encoded genes. In \u003cem\u003eArabidopsis\u003c/em\u003e, TE sequences are associated with 7.8% of expressed genes, with 1.2% potentially contributing to protein-coding regions\u003csup\u003e\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e\u003c/sup\u003e. There are likely many additional genes that have escaped detection due to sequence divergence, obscuring their similarity to transposases\u003csup\u003e\u003cspan citationid=\"CR58\" class=\"CitationRef\"\u003e58\u003c/span\u003e,\u003cspan citationid=\"CR59\" class=\"CitationRef\"\u003e59\u003c/span\u003e\u003c/sup\u003e. Moreover, in most cases, the function of these genes remains unknown, raising the question of whether each gene has acquired a distinct role or if there are shared functions among them. To address this, we conducted statistical and enrichment analyses on genes domesticated from TEs. In contrast to ncRNAs, as shown in Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eD, over three-quarters of the genes domesticated from TEs overlap with class I TEs, with the \u003cem\u003eCopia\u003c/em\u003e family being the most prevalent, accounting for 44%. Using all TE-overlapping genes as a background, we subsequently performed a functional enrichment analysis for genes related to each TE superfamily. The top ten significantly enriched functional gene families were mapped to their corresponding TE superfamilies to create a network, as shown in Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eE. Terms such as \u0026lsquo;nucleic acid,\u0026rsquo; \u0026lsquo;binding DNA integration,\u0026rsquo; \u0026lsquo;zinc ion binding,\u0026rsquo; \u0026lsquo;DNA binding,\u0026rsquo; \u0026lsquo;ATP binding,\u0026rsquo; \u0026lsquo;RNA-DNA hybrid ribonuclease activity,\u0026rsquo; and \u0026lsquo;protein binding\u0026rsquo; were significantly enriched in both Class I and class II superfamilies, while \u0026lsquo;DNA helicase,\u0026rsquo; \u0026lsquo;DNA repair,\u0026rsquo; \u0026lsquo;sequence-specific DNA binding,\u0026rsquo; \u0026lsquo;telomere maintenance,\u0026rsquo; and \u0026lsquo;DNA-mediated transposition\u0026rsquo; were enriched in class II TE superfamilies. Finally, statistics on DNA repair genes in various genomes indicate that, as shown in Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eF, these genes are abundant in most higher plants and particularly rich in certain angiosperms (such as the \u003cem\u003eArachis genus\u003c/em\u003e). In summary, class I TE superfamilies transposase genes are the primary source of TE-origin genes, and the functional genes derived from each TE superfamily exhibit strong family-specific characteristics.\u003c/p\u003e \u003cp\u003eGene Duplications Induced by TEs\u003c/p\u003e \u003cp\u003eIn the context of adaptation, the expansion of gene families can lead to the functional diversification of genes, which is crucial for adapting to new environments \u003csup\u003e\u003cspan additionalcitationids=\"CR61 CR62 CR63\" citationid=\"CR60\" class=\"CitationRef\"\u003e60\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR64\" class=\"CitationRef\"\u003e64\u003c/span\u003e\u003c/sup\u003e. TEs are major drivers of gene family expansion. Here, integrating the similarity information of genes and upstream/downstream TEs, we identified 10,488,967 TE-induced gene duplications, accounting for 40.83% of the total genes. Our statistics indicate that, as shown in Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eG, over 80% of the duplicated genes were induced by Class II TEs, with \u003cem\u003eHelitron\u003c/em\u003e being the most prevalent, accounting for 21%, followed by \u003cem\u003eMutator\u003c/em\u003e. Many TEs cluster into TE islands, which supports the idea that functional genomic regions are frequently revisited by TEs\u003csup\u003e\u003cspan citationid=\"CR48\" class=\"CitationRef\"\u003e48\u003c/span\u003e\u003c/sup\u003e. Using all TE-induced duplication genes as a background, we subsequently performed a functional enrichment analysis for genes related to each TE superfamily. Figure\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eH shows the top 20 significantly enriched functional gene families, and biosynthetic function genes were significantly enriched in both the class I and class II superfamilies, with the total proportion of each TE family exceeding 100%, suggesting that different TE families might collaborate in the gene duplication process. \u0026lsquo;Phototropism\u0026rsquo; was enriched in class I \u003cem\u003eGypsy\u003c/em\u003e, and \u0026lsquo;meristem maintenance\u0026rsquo; is significantly enriched in both \u003cem\u003eHelitron\u003c/em\u003e and \u003cem\u003eMutator\u003c/em\u003e, a phenomenon also observed in recently active TEs. \u0026lsquo;Double-strand break repair\u0026rsquo; was significantly enriched in both \u003cem\u003eHelitron\u003c/em\u003e and CACTA, indicating that these gene families may participate in the transposition process of these TEs. Finally, statistics on meristem development genes in various genomes indicate that, as shown in Fig.\u0026nbsp;\u003cspan refid=\"Fig2\" class=\"InternalRef\"\u003e2\u003c/span\u003eI, these genes are abundant in most higher plants and particularly rich in some angiosperms (such as \u003cem\u003eUrochloa decumbens\u003c/em\u003e).\u003c/p\u003e \u003cp\u003eTransposed duplications are prevalent among disease resistance gene homologs\u003csup\u003e\u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e32\u003c/span\u003e\u003c/sup\u003e, indicating that there may be nonrandom, recurrent patterns in the origin of gene family members across diverse evolutionary lineages. Ther has been more than one burst for each TE family over several million years\u003csup\u003e\u003cspan citationid=\"CR65\" class=\"CitationRef\"\u003e65\u003c/span\u003e\u003c/sup\u003e. When a TE captures a functional gene and subsequently bursts, it can facilitate the expansion of the functional gene family (Fig.\u0026nbsp;\u003cspan refid=\"Fig1\" class=\"InternalRef\"\u003e1\u003c/span\u003eD). Here, by comparing gene family expansion across different lineages, we identified 1,097 bursts (genes of a family duplicated over 100 times) involving 114 species \u003cb\u003e(Table \u003cspan refid=\"MOESM6\" class=\"InternalRef\"\u003eS6\u003c/span\u003e)\u003c/b\u003e. Among these, \u003cem\u003eOryza sativa\u003c/em\u003e presented the greatest number of bursts, occurring 24 times, followed by \u003cem\u003eBrassica oleracea\u003c/em\u003e with 20 bursts. In terms of TE superfamily comparisons, \u003cem\u003eHelitron\u003c/em\u003e was the most common, with 396 bursts, followed by \u003cem\u003eGypsy\u003c/em\u003e with 311 bursts. The gene families involved mainly include those related to ATP synthase and metabolism, meristem development, phototropism, and telomere maintenance, among others.\u003c/p\u003e\n\u003ch3\u003eUnderstanding the Roles of TEs in Plant Evolution\u003c/h3\u003e\n\u003cp\u003eIn plants, compact series of rather recent speciation events are typically exemplified by pangenome sequencing projects \u003csup\u003e40\u0026ndash;43,66\u0026minus;71\u003c/sup\u003e. However, it is not well known when and how these species have diversified; therefore, this topic has been an issue of profound interest that has yet to be resolved. According to Darwin\u0026rsquo;s perspective, evolution can be restated as a process in which genomes generate genetic innovations, which are then selected by the environment and incorporated into the genome, ultimately leading to the emergence of new species \u003csup\u003e\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e,\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e\u003c/sup\u003e. This can be further broken down into two key questions: What unique functional innovations are found in different plant lineages? How are these functions acquired? To address the first question, As shown in Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003eA, we begin by grouping plant species according to their evolutionary lineages and then constructing a 558 \u0026times; 72,537 matrix on the basis of the number of functional genes/ncRNAs in each genome. Through supervised machine learning classification, we assess the importance of each functional family. Combined with statistical tests of interpopulation differences, this approach allows us to identify functional features specific to each plant group. Thus, by conducting cross-species comparisons and analyzing functional genes significantly influenced by TEs, we can partially address the second question.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eRevealing the Contribution of TEs to Angiosperm Evolution\u003c/p\u003e \u003cp\u003eTo identify characteristic functional gene families of angiosperms, we first classified 352 species into five groups on the basis of evolutionary lineage: algae, mosses, ferns, gymnosperms, and angiosperms. Next, we compared the angiosperm group with the other four groups in pairs, and used a random forest machine learning classifier to select the characteristic functional families of angiosperms. We then used Student's t test to assess the significance of differences in each characteristic among the groups Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003eA \u003cb\u003eand Table \u003cspan refid=\"MOESM7\" class=\"InternalRef\"\u003eS7\u003c/span\u003e\u003c/b\u003e. Finally, we identified 22 TE-associated functional gene families and 5 TE-associated ncRNA families. Figure\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003eB shows the average gene numbers of these gene families in each group, indicating that 8 of these functional gene families are exclusive to angiosperms, such as cyclin D6, whereas other functional gene families have significantly greater member numbers in angiosperms than in the other groups. Furthermore, we selected three functional gene families. By analyzing TE-mediated gene duplications and the proportion of TE-origin genes (Fig.\u0026nbsp;\u003cspan refid=\"Fig3\" class=\"InternalRef\"\u003e3\u003c/span\u003eC), we found that TEs primarily mediate gene duplication in the Cyclin D6 functional gene family. In contrast, TEs may provide functional elements and mediate gene duplication in the genetic innovations of the FAR1, zinc finger SWIM3, and MYB transcription factor gene families (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003e), all of which are specific to the angiosperm lineage (Fig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003eB). FAR1 genes are domesticated from Mutator-like transposases (MULEs), research on \u003cem\u003eArabidopsis\u003c/em\u003e reported they regulate phytochrome A signaling\u003csup\u003e\u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e,\u003cspan citationid=\"CR72\" class=\"CitationRef\"\u003e72\u003c/span\u003e,\u003cspan citationid=\"CR73\" class=\"CitationRef\"\u003e73\u003c/span\u003e\u003c/sup\u003e. We also found that the zinc finger SWIM3 transcription factors derived from Mutator, and MYB transcription factors derived from CACTA transposase, have undergone significant expansion in angiosperms\u003csup\u003e\u003cspan citationid=\"CR74\" class=\"CitationRef\"\u003e74\u003c/span\u003e\u003c/sup\u003e, which control chloroplast biogenesis\u003csup\u003e\u003cspan citationid=\"CR75\" class=\"CitationRef\"\u003e75\u003c/span\u003e\u003c/sup\u003e\u003cb\u003e(\u003c/b\u003eFig.\u0026nbsp;\u003cspan refid=\"Fig4\" class=\"InternalRef\"\u003e4\u003c/span\u003eC\u003cb\u003e)\u003c/b\u003e.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eNext, we further analyzed the functional gene family characteristics of monocots and dicots via this functional family screening process, with relevant results shown in (\u003cb\u003eTable \u003cspan refid=\"MOESM7\" class=\"InternalRef\"\u003eS7\u003c/span\u003e\u003c/b\u003e, Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e \u003cb\u003eand Fig \u003cspan refid=\"MOESM3\" class=\"InternalRef\"\u003eS3\u003c/span\u003e\u003c/b\u003e). In dicots, a horizontal comparison across seven families, as shown in Fig.\u0026nbsp;\u003cspan refid=\"Fig5\" class=\"InternalRef\"\u003e5\u003c/span\u003e, revealed that enzymes are the most prevalent among the family-specific functional genes, accounting for 52.34%, and transcription factors accounting for 8.77%. In monocots, as shown in \u003cb\u003eFig \u003cspan refid=\"MOESM3\" class=\"InternalRef\"\u003eS3\u003c/span\u003e\u003c/b\u003e, various enzymes accounting for 47.5% and transcription factors accounting for 9.17%, Vertical analysis of four key evolutionary nodes in rice revealed that the evolution from monocots to the family \u003cem\u003ePoaceae\u003c/em\u003e and then to the subfamily \u003cem\u003eOryza\u003c/em\u003e was associated with the development of new gene functions. In the final stage of cultivated rice, the top 10 functional genes are related to an increase in quantity. Overall, this study identified 1563 gene family characteristics unique to different lineages of angiosperms, with various enzymes accounting for 49.52% and transcription factors accounting for 9.08%, which allows us to trace the contribution of TEs to genetic functional innovation across various stages and branches of plant evolution.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e \u003cp\u003eComprehending Routes of Synthase Evolution\u003c/p\u003e \u003cp\u003eTE-free genes are involved in critical functions such as development, transcription, and the regulation of transcription, whereas TE-rich genes are involved in functions such as transport and metabolism, which could be explained by a stronger selection pressure acting on both the coding and noncoding regions of TE-free genes than on those of TE-rich genes\u003csup\u003e\u003cspan citationid=\"CR76\" class=\"CitationRef\"\u003e76\u003c/span\u003e\u003c/sup\u003e. In line with this observation, various enzymes make up nearly half of the TE-associated gene families, with synthases being the most prevalent, with 16 out of 18 being terpenoid synthases, which play roles in defense and growth regulation. To gain a deeper understanding of the impact of TEs on synthase gene families, we conducted a comprehensive analysis of 18 synthase gene families, that were lineage specific \u003cb\u003e(\u003c/b\u003eFig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003eA). The first 9 gene families are specific to dicot lineages, whereas the remaining 9 are specific to monocot lineages. Notably, K14037 ent-sandaracopimaradiene/labdatriene synthase is specific to the monocot lineage (\u003cem\u003eOryzoideae\u003c/em\u003e), yet in a dicot (Heracleum sosnowskyi), there are up to 100 genes in this family. Moreover, K14037-related proteins have not been annotated in Daucus carota or other dicots within \u003cem\u003eApiaceae\u003c/em\u003e, suggesting that this protein family in Heracleum sosnowskyi may have originated from TE-mediated horizontal gene transfer \u003cb\u003e(\u003c/b\u003eFig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003eB\u003cb\u003e)\u003c/b\u003e, moreover, TE annotation of gene regions shows that the expansion of this gene family is TE-mediated \u003cb\u003e(\u003c/b\u003eFig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e6\u003c/span\u003eC\u003cb\u003e).\u003c/b\u003e Notably, class I \u003cem\u003eCopia\u003c/em\u003e-induced duplication genes have only 1 exon, whereas class II \u003cem\u003eMutator\u003c/em\u003e-induced duplication genes have 3 exons (\u003cb\u003eFig \u003cspan refid=\"MOESM4\" class=\"InternalRef\"\u003eS4\u003c/span\u003e\u003c/b\u003e), which aligns with stress-responsive genes located near the TE families tend to be substantially shorter in length with fewer introns\u003csup\u003e\u003cspan citationid=\"CR77\" class=\"CitationRef\"\u003e77\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003cp\u003e \u003c/p\u003e"},{"header":"Discussion","content":"\u003cp\u003eIn this study, we propose a machine learning-based framework to identify key genetic innovation events associated with TEs. We performed a comprehensive identification of TEs across 558 genomes on the basis of integrated functional genomic annotations, resulting in a large dataset of TE-associated genetic innovation events across 352 species. This includes the generation of new functional genes by domesticated transposases, the production of ncRNAs, and TE-mediated gene duplications and gene family expansions, which are significantly enriched in 2,805 functional terms. We then grouped the genomes according to their genetic lineages, combining feature selection through machine learning and population difference analysis to identify lineage-specific functional features. Finally, we integrated lineage-specific genetic factors with TE-related genetic innovations to determine the contributions of TEs to lineage-specific genetic functional innovations and infer the role of TEs in plant functional genomic evolution. We conclude that enzymes (e.g., synthases) and chromatin-related factors (e.g., transcription factors) exhibit functional innovations with TEs playing a significant role in plant evolution. Our study and results validated and refined McClintock\u0026rsquo;s observations and hypotheses\u003csup\u003e\u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e\u003c/sup\u003e through large-scale comparative studies across species, providing a new method for research on TEs in the context of plant evolution.\u003c/p\u003e \u003cp\u003eAngiosperms, the most diverse group of flowering plants, exhibit a wide range of functional characteristics that reflect their adaptations to various environmental conditions and growth scenarios. This study systematically analyzes the lineage-specific functional genes of two angiosperm classes (dicots and monocots) across eight families and examines the role of TEs in the evolution of these functional genes. Our results revealed that during the early stages of evolution, TE-associated genetic innovations were observed in cyclin D6 and transcription factors, such as FAR1 genes, which regulate phytochrome A signaling and are derived from Mutator-like transposases (MULEs) \u003csup\u003e\u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e,\u003cspan citationid=\"CR72\" class=\"CitationRef\"\u003e72\u003c/span\u003e,\u003cspan citationid=\"CR73\" class=\"CitationRef\"\u003e73\u003c/span\u003e\u003c/sup\u003e. In later stages, functional innovations became prominent in enzyme-encoding gene families, particularly in various synthetases, which is reflected in the diverse functional properties of secondary metabolites in plants. This fundamental genomic understanding is likely to be valuable for crop improvement. Oliver \u003cem\u003eet al.\u003c/em\u003e documented 65 examples of TE insertions in regulatory or coding sequences that affect a wide range of phenotypic traits, such as skin color in grapes\u003csup\u003e\u003cspan citationid=\"CR78\" class=\"CitationRef\"\u003e78\u003c/span\u003e\u003c/sup\u003e and anthocyanin accumulation in blood oranges\u003csup\u003e\u003cspan citationid=\"CR79\" class=\"CitationRef\"\u003e79\u003c/span\u003e\u003c/sup\u003e, highlighting the importance of genome-wide neofunctionalization in generating new variations\u003csup\u003e\u003cspan citationid=\"CR80\" class=\"CitationRef\"\u003e80\u003c/span\u003e\u003c/sup\u003e. Analysis of lineage-specific functional genes at different evolutionary stages in \u003cem\u003eOryzoideae\u003c/em\u003e suggests that TE-associated miRNAs may have played a role in the evolution of this group, indicating that the evolution and selection of small RNAs are potentially important processes in crop plants, including rice\u003csup\u003e\u003cspan citationid=\"CR81\" class=\"CitationRef\"\u003e81\u003c/span\u003e,\u003cspan citationid=\"CR82\" class=\"CitationRef\"\u003e82\u003c/span\u003e\u003c/sup\u003e and corn\u003csup\u003e\u003cspan citationid=\"CR80\" class=\"CitationRef\"\u003e80\u003c/span\u003e\u003c/sup\u003e. In addition to known cases where TE insertions or duplicated genes affect plant traits, the broader significance of these events is increasingly recognized, even when the specific mechanisms are not fully understood. Further research is needed to harness this biological knowledge to enhance traits of agronomic importance.\u003c/p\u003e \u003cp\u003eOwing to their inherent ability to carry and integrate DNA into foreign genomes, transposable elements (TEs) are widely used tools in genetic engineering\u003csup\u003e\u003cspan citationid=\"CR83\" class=\"CitationRef\"\u003e83\u003c/span\u003e\u003c/sup\u003e. To optimize TE-based genetic tools and design effective strategies, it is essential to systematically understand the roles of TEs as \u0026ldquo;nature\u0026rsquo;s genetic engineers\u0026rdquo;. This study systematically assessed the roles and patterns of TEs in functional genomic innovations in plants, identifying 1,258,230 genes originating from TEs, 1,165,059 ncRNAs derived from TEs, and 10,488,967 TE-induced gene duplications \u003cb\u003e(Table \u003cspan refid=\"MOESM2\" class=\"InternalRef\"\u003eS2\u003c/span\u003e)\u003c/b\u003e. This resource is particularly valuable for those interested in understanding the factors underlying transposition activity and evolutionary dynamics, as well as for expanding the TE toolbox. Our results indicate that TE-induced gene duplications, followed by mutations and natural selection, predominantly generate new functions. Analysis of lineage-specific functional genes affected by TEs revealed that transcription factors and synthetases are the most impacted categories. Specifically, an analysis of TE-associated synthases revealed that TEs capture certain terpene synthases, mediating gene family expansion within species and potentially facilitating horizontal gene transfer related to K14037 genes. A similar phenomenon has been observed in the horizontal transfer of BtPMaT1 between plants and whiteflies\u003csup\u003e\u003cspan citationid=\"CR84\" class=\"CitationRef\"\u003e84\u003c/span\u003e\u003c/sup\u003e. The extent and dynamics of horizontal gene transfer mediated by TEs between species warrant further investigation.\u003c/p\u003e \u003cp\u003eThis study contributes significantly to our understanding of how TEs drive plant genome evolution. An analysis of high-quality genomic assemblies from 352 species across five plant phyla, revealed the extensive role of TEs in generating genetic diversity. The comprehensive identification of more than 460\u0026nbsp;million TEs and their associated transposase domains, along with their impacts on genes and ncRNAs, reveals how TEs contribute to the creation of new genes and gene duplications. This not only enhances our grasp of the evolutionary processes influenced by TEs but also identifies 2,805 functional gene families, with 1563 likely crucial at key evolutionary stages. This study highlights the critical role of TEs as \u0026lsquo;nature\u0026rsquo; genetic engineers\u0026rsquo; and suggests that understanding TE-driven adaptive evolution can guide improvements in synthetic biology tools and strategies. Insights into the evolutionary pathways of synthetic enzymes, informed by TE dynamics, could lead to advancements in synthetic biology. This set the stage for future research to validate these evolutionary roles, explore their impact in various environmental contexts, and integrate these insights into applications in crop improvement and biotechnology. Continued advancements in sequencing technologies and genomic data analysis will further refine our understanding of TE dynamics and their contributions to plant evolution.\u003c/p\u003e"},{"header":"Materials and methods","content":"\u003cdiv id=\"Sec8\" class=\"Section2\"\u003e \u003ch2\u003eCharacterization and Annotation of TEs\u003c/h2\u003e \u003cp\u003eData collection\u003c/p\u003e \u003cp\u003eHigh-quality genomes provide a direct and reliable avenue for the comprehensive identification of TEs and tracing their proliferation and activity. In pursuit of this objective, we amassed a collection of 558 publicly available reference-quality genomes on the basis of four distinct criteria: 1) they belong to species of significant importance; 2) the assembly level is at least at the chromosome level; and 3) complete functional gene annotations are available. The genomes and their functional gene annotations were downloaded from the databases listed in \u003cb\u003eTable \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003e (accessed on June 20, 2024)\u003c/b\u003e. We conducted a genome evaluation on the downloaded genomes (Table \u003cspan refid=\"MOESM1\" class=\"InternalRef\"\u003eS1\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eTransposable elements annotation\u003c/p\u003e \u003cp\u003eTEs were identified via a method that combines \u003cem\u003ede novo\u003c/em\u003e structure analyses and homology from two repeat detection programs Extensive \u003cem\u003ede novo\u003c/em\u003e TE Annotator software version 2.0.1 (EDTA) \u003csup\u003e\u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e44\u003c/span\u003e\u003c/sup\u003e. EDTA incorporates LTRharvest, LTR_FINDER, LTR_retriever, TIR-Learner, HelitronScanner, RepeatModeler, and RepeatMasker, as well as customized filtering scripts for \u003cem\u003ede novo\u003c/em\u003e identification of each TE class, and compiles the results into a comprehensive TE library. The RepeatMasker (version 4.0.5)\u003csup\u003e\u003cspan citationid=\"CR85\" class=\"CitationRef\"\u003e85\u003c/span\u003e\u003c/sup\u003e and the final EDTA repeat libraries were subsequently used to soft mask the genome assemblies prior to annotation. Because RepeatMasker reported identity. Young TEs and aged TEs are defined as annotations that are \u0026gt;\u0026thinsp;95% identical to the intact TE entries, or \u0026lt;\u0026thinsp;95% identical, respectively.\u003c/p\u003e \u003cp\u003eNext, to identify protein or nucleic acid sequence homology to proteins encoded by diverse families of transposable elements, we used homology searching of the 558 genome assembled sequences against curated conserved ORFs of TEs using TransposonPSI (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttp://transposonpsi.sourceforge.net/\u003c/span\u003e\u003cspan address=\"http://transposonpsi.sourceforge.net/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e)\u003csup\u003e46\u003c/sup\u003e with the parameter \u0026lsquo;nuc\u0026rsquo;. The best hits were realigned via exonerate, and the proteins with TE copies were extracted.\u003c/p\u003e \u003cp\u003eGene and ncRNA annotation\u003c/p\u003e \u003cp\u003eProtein domains were predicted using InterProScan\u003csup\u003e\u003cspan citationid=\"CR86\" class=\"CitationRef\"\u003e86\u003c/span\u003e\u003c/sup\u003e (v.4.8) based on the InterPro (v.32.0) (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttp://www.ebi.ac.uk/interpro/\u003c/span\u003e\u003cspan address=\"http://www.ebi.ac.uk/interpro/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e) database, which also provides a portal for obtaining GO terms (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttp://geneontology.org/\u003c/span\u003e\u003cspan address=\"http://geneontology.org/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttp://www.geneontology.org/page/go-database\u003c/span\u003e\u003cspan address=\"http://www.geneontology.org/page/go-database\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e)\u003csup\u003e87\u003c/sup\u003e. Pathways of the genes were identified via BLAST searches against the Kyoto Encyclopedia of Genes and Genomes (KEGG; \u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://www.genome.jp/kegg/\u003c/span\u003e\u003cspan address=\"https://www.genome.jp/kegg/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e) database\u003csup\u003e\u003cspan citationid=\"CR88\" class=\"CitationRef\"\u003e88\u003c/span\u003e\u003c/sup\u003e. TFs were identified by performing BLASTP searches against the plant transcription factor database PlantTFDB version 5.0 (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttp://planttfdb.gao-lab.org/\u003c/span\u003e\u003cspan address=\"http://planttfdb.gao-lab.org/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e )\u003csup\u003e89\u003c/sup\u003e. Flowering time genes were annotated based on FLOR-ID\u003csup\u003e\u003cspan citationid=\"CR90\" class=\"CitationRef\"\u003e90\u003c/span\u003e\u003c/sup\u003e. For noncoding RNA prediction, Infernal \u003csup\u003e\u003cspan citationid=\"CR91\" class=\"CitationRef\"\u003e91\u003c/span\u003e\u003c/sup\u003e(v1.1.5) was used to identify ncRNAs on the basis of the Rfam database\u003csup\u003e\u003cspan citationid=\"CR92\" class=\"CitationRef\"\u003e92\u003c/span\u003e\u003c/sup\u003e.\u003c/p\u003e \u003c/div\u003e\n\u003ch3\u003eAssessing the impact of TEs on the Host Genome\u003c/h3\u003e\n\u003cp\u003eAssessed co-locations or overlapping with other genomic features\u003c/p\u003e \u003cp\u003eThe genomic TEs and transposase domains were categorized as being in gene regions (overlapping with a functional protein), upstream and downstream regions (within a 2-kb region upstream or downstream from the transcription start site), and ncRNA regions (overlapping with a ncRNA). For each genome assembly, the overlap of TEs with different genomic features was performed using BEDtools\u003csup\u003e\u003cb\u003e\u003cspan citationid=\"CR93\" class=\"CitationRef\"\u003e93\u003c/span\u003e\u003c/b\u003e\u003c/sup\u003e, which intersects with the parameter \u0026ldquo;-f 0.5\u0026rdquo; and the number of TEs by superfamily (i.e., summing independently for \u003cem\u003eCopia, Gypsy\u003c/em\u003e, CACTA, hAT, \u003cem\u003eMutator\u003c/em\u003e, \u003cem\u003eTc1-Mariner, PIF-Harbinger, Helitron\u003c/em\u003e, and other unclassified TEs) was determined.\u003c/p\u003e \u003cp\u003eDetection of domesticated transposases and TEs\u003c/p\u003e \u003cp\u003eThe selection of domesticated transposases and TEs is divided into two steps:\u003c/p\u003e \u003cp\u003eStep 1: Identify genes that overlap with transposase domains as candidates for domesticated transposases, and ncRNAs that overlap with TEs as candidates for ncRNAs originating from TEs.\u003c/p\u003e \u003cp\u003eStep 2: Count the number of species within 352 species that contain the gene/ncRNA family, as well as the number of species with evidence of domesticated TEs. If the proportion of species with evidence is greater than 50%, they are considered likely to originate from TEs.\u003c/p\u003e \u003cp\u003eDetect TE induced gene duplications\u003c/p\u003e \u003cp\u003eA modified DupGen_finder pipeline was used to identify gene duplications\u003csup\u003e\u003cspan citationid=\"CR94\" class=\"CitationRef\"\u003e94\u003c/span\u003e\u003c/sup\u003e. Briefly, all-versus-all BLASTP was performed via OrthoFinder to search for potential homologous gene pairs. DupGen_finder was then used to identify whole-genome duplication (WGD), proximal duplication (PD), tandem duplication (TD), transposed duplication (TRD), and dispersed duplication (DSD) gene pairs. For further analysis, we focused only on TRD and DSD genes, as WGD, PD and TD duplicates may not have been caused by TEs. Next, we filtered out gene pairs without TE evidence support (requiring cosine similarity\u0026thinsp;\u0026gt;\u0026thinsp;0.5 of TE components between the two genes of each gene pair). Finally, for each functional gene family, we counted the number of family genes in each species and the number of TE-mediated duplicated genes. We then assessed the impact of TEs on the expansion of functional gene families by evaluating the correlation between these two factors.\u003c/p\u003e\n\u003ch3\u003eAssessing the impact of TEs on genetic functions of plants\u003c/h3\u003e\n\u003cp\u003eGene and ncRNA enrichment analysis\u003c/p\u003e \u003cp\u003eTo investigate the interplay between TEs and the host genome, we conducted enrichment analyses focusing on genes and ncRNAs associated with TEs. First, for functional genes, enrichment analyses were performed via GO annotations, KEGG annotations, PlantTF annotations, and FLOR annotations. For ncRNAs, enrichment analysis was based on ncRNA families. Second, the choice of background genes varied depending on the analysis objectives. To analyze the impact of each TE superfamily on genetic features, we used all TE-associated genes as the background and performed enrichment analyses for each superfamily-associated gene. To study the effects of TEs on plant evolution, we used all functional genes as the background and conducted enrichment analyses for TE-associated genes. The Python package GSEApy\u003csup\u003e\u003cspan citationid=\"CR95\" class=\"CitationRef\"\u003e95\u003c/span\u003e\u003c/sup\u003e was used for enrichment analysis, with a P value less than 0.01 indicating significant enrichment.\u003c/p\u003e \u003cp\u003eMachine Learning for Identifying Plant Lineage-Specific Functional Features\u003c/p\u003e \u003cp\u003eThe process of selecting lineage-specific functional gene features consists of four main steps: Step 1. The number of genes in each functional gene family for 558 genomes was counted, creating a 558 \u0026times; 72,537 matrix. Step 2. All genomes were grouped according to their evolutionary lineage, for example, all species were divided into algae, mosses, ferns, gymnosperms, and angiosperms. Step 3. The matrix and grouping data were fed into a random forest model as training data and the importance of each feature as output. Step 4. Furthermoer, Student's t-test was used to assess the significance of differences for each feature among the groups, retaining features with importance\u0026thinsp;\u0026gt;\u0026thinsp;0 that were significantly different across all groups.\u003c/p\u003e \u003cp\u003ePhylogenetic analysis\u003c/p\u003e \u003cp\u003eThe taxonomic information was retrieved from the NCBI page of each genome, with manual determination for those taxa not found in NCBI page. The phylogenetic cladogram was reconstructed based on the taxonomical NCBI level of all genomes surveyed in this analysis using the NCBITaxa in the Python Environment for Tree Exploration3 (ETE3) v3.1.12 program \u003csup\u003e\u003cspan citationid=\"CR96\" class=\"CitationRef\"\u003e96\u003c/span\u003e\u003c/sup\u003e. iTOL\u003csup\u003e\u003cspan citationid=\"CR97\" class=\"CitationRef\"\u003e97\u003c/span\u003e\u003c/sup\u003e was used to visualize the phylogenetic tree.\u003c/p\u003e"},{"header":"Declarations","content":"\u003ch3\u003eAcknowledgements\u003c/h3\u003e\n\u003cp\u003eNot applicable.\u003c/p\u003e\n\u003ch3\u003eAuthors\u0026apos; contributions\u003c/h3\u003e\n\u003cp\u003eLX and HY conceived and designed the study. HY performed computational analyses with the help of LX. HY analyzed and interpreted the genome data regarding the evolution of TEs and their host genomes. HY, SSK, SCC, SS and LX were all contributors in writing the manuscript. All authors read and approved the final manuscript.\u0026nbsp;\u003c/p\u003e\n\u003ch3\u003eFunding\u003c/h3\u003e\n\u003cp\u003eLX is supported by National Key Research and Development Program of China, grant number 2021YFD2200502. The authors have declared that no conflict of interest exists.\u003c/p\u003e\n\u003ch3\u003eAvailability of data and materials\u003c/h3\u003e\n\u003cp\u003eThe codes/datasets generated during the current study are available in the Github repository, https://github.com/Color4/TE_Evolution_in_Plants/.\u003c/p\u003e\n\u003ch3\u003eEthics approval and consent to participate\u003c/h3\u003e\n\u003cp\u003eNot applicable.\u003c/p\u003e\n\u003ch3\u003eConsent for publication\u003c/h3\u003e\n\u003cp\u003eNot applicable.\u003c/p\u003e\n\u003ch3\u003eCompeting interests\u003c/h3\u003e\n\u003cp\u003eThe authors declare that they have no competing interests.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n\u003cli\u003eBourque, G.\u003cem\u003e et al.\u003c/em\u003e Ten things you should know about transposable elements. \u003cem\u003eGenome Biology\u003c/em\u003e \u003cstrong\u003e19\u003c/strong\u003e, doi:10.1186/s13059-018-1577-z (2018).\u003c/li\u003e\n\u003cli\u003eQuesneville, H. 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ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data. \u003cem\u003eMolecular Biology and Evolution\u003c/em\u003e \u003cstrong\u003e33\u003c/strong\u003e, 1635-1638, doi:10.1093/molbev/msw046 (2016).\u003c/li\u003e\n\u003cli\u003eLetunic, I. \u0026amp; Bork, P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. \u003cem\u003eNucleic Acids Research\u003c/em\u003e \u003cstrong\u003e49\u003c/strong\u003e, W293-W296, doi:10.1093/nar/gkab301 (2021).\u003c/li\u003e\n\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":"Transposable elements, Genome evolution, Plant, Computational biology and bioinformatics","lastPublishedDoi":"10.21203/rs.3.rs-5428092/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-5428092/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003eTransposable elements (TEs), nature’s genetic engineers’, are pivotal drivers of genome evolution, yet their precise mechanisms in shaping plant functional innovation remain elusive. This study presents a comprehensive analysis of TEs across 558 high-quality plant genomes, encompassing 352 species from 221 genera across five phyla, ranging from algae to angiosperms. We identified over 460\u0026nbsp;million TEs and 67\u0026nbsp;million transposase domains, systematically assessing their impact on host genomes through gene domestication, noncoding RNA generation, and gene duplication. Our analysis revealed 1,258,230 genes domesticated from TEs, 1,165,059 ncRNAs originating from TEs, and 10,488,967 TE-induced gene duplications. These genes affect more than 2,805 function families, likely planning crucial roles at key stages of plant evolution. Using a machine learning-based framework, we uncovered 1,536 lineage-specific functional gene families significantly influenced by TEs, with enzymes and transcription factors being predominant. Notably, we elucidated the role of TEs in expanding transcription factor gene families and in facilitating potential horizontal gene transfer of synthase gene families. This study provides unprecedented insights into TE-driven plant evolution, demonstrating how TEs contributes to key innovations at various evolutionary stages. Our finding not only enhance understanding of plant genome dynamics but also offer valuable resources for crop improvement and synthetic biology, illumination both current knowledge and future potential of evolutionary processes.\u003c/p\u003e","manuscriptTitle":"Machine learning based pan-plant analyses of transposable elements across 352 species illuminates genome evolution","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-11-28 17:07:47","doi":"10.21203/rs.3.rs-5428092/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":"4343c03e-f70e-423b-baa8-ea60069c37ec","owner":[],"postedDate":"November 28th, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2025-09-22T15:54:53+00:00","versionOfRecord":[],"versionCreatedAt":"2024-11-28 17:07:47","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-5428092","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-5428092","identity":"rs-5428092","version":["v1"]},"buildId":"qtupq5eGEP_6zYnWcrvyt","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}