A high-quality mitochondrial genome of Suriana maritima reveals tremendous gene transfers between the plastid and mitochondrial genomes

A high-quality mitochondrial genome of Suriana maritima reveals tremendous gene transfers between the plastid and mitochondrial genomes | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article A high-quality mitochondrial genome of Suriana maritima reveals tremendous gene transfers between the plastid and mitochondrial genomes Jian-Xin Li, Runxian Yu, Ze-Long Nie, Meng hua Zhang, Miao-Miao Shi, and 6 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-3948491/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract Background Gene transfer between the plastid and mitochondrial genomes has been reported in several lineages of the legume family (Leguminosae or Fabaceae). However, it is not clear whether these events happened in other families of the order Fabales. We herein generated a high-quality mitochondrial genome of Suriana maritima in the family Surianaceae, which is closely related to Leguminosae and distributed mainly in extreme environments of tropical coral islands, to understand the gene transfers between orgenelle genomes of S. maritima and the structural and functional evolution of mitogenomes in Fabales. Results We combined Illumina and Nanopore technologies to assemble the mitogenome of S. maritima . The mitogenome was 458,738 bp in length and contained 39 protein-coding, three ribosomal RNA, and 20 transfer RNA genes. A number of sequences derived from the chloroplast genome of S. maritima were detected in the mitogenome, including 41 plastid genes among 83 mitochondrial plastid DNA sequences with a total length of 30,834 bp. Transferred genes accounted for 18.8% of the plastid genome and 6.7% of the mitogenome, and these estimates were much higher than those in previous studies of Fabales. Conclusions In addition to providing a high-quality mitogenome of an additional species in Fabales and the first species in Surianaceae, S. maritima , our findings advance our understanding of gene transfer between organelle genomes. Gene transfer Fabales mitochondrial genome Suriana maritima Surianaceae Figures Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Background The plant mitogenome is mainly assembled into a circular structure containing all genes [ 1 ], generally known as the “master circle”, with a few exceptions as linear, branched, overlapping, or multiple coexisting structures [ 2 – 5 ]. Redundant sequences and extensive genomic recombination make it difficult to recover the conformation of the plant mitogenome. In particular, it is difficult to correctly assemble the mitogenome based on second-generation sequencing data and accurately evaluate mitogenome evolution, including codon usage, RNA editing, horizontal transfer, gene loss and acquisition [ 6 ]. Among these, intracellular gene transfer has been found in several lineages of plants. For example, the genome transferred from plastid to mitochondrion span 1.67 kb in Silene (Caryophyllaceae) and 3.52 kb in Vigna radiata (Fabaceae) [ 7 ]. The total length of Bupleurum chinense (Apiaceae) sequence transferred from the plastid genome to the mitogenome is 11,144 bp, accounting for 2.56% of the mitogenome [ 8 ]. However, analyses of gene transfer between the plastid, mitochondrial, or nuclear genomes in a broader range of taxa are needed, including species closely related to legumes are lacking. Fabales contains four families, namely Leguminosae, Polygallaceae, Quillajaceae and Surianaceae [ 10 ]. Surianaceae is a small family with only five woody genera and eight species distributed in pantropical areas, and, in particular, in Australia and Mexico [ 11 , 12 ]. Suriana maritima L. is the member of Surianaceae and shows with an extensive distribution in the tropical coral islands and coastal zones. In China, it is only found on the Xisha Islands and Dongsha Islands (coral islands) in the South China Sea, mainly growing on the sandy land or rock cracks, as a pioneer species [ 13 , 14 ]. In this study, we assembled a high-quality mitogenome of S. maritima using both Illumina and Nanopore technologies and analyzed its genomic and structural features as well as the role of gene transfer from plastids. This study provides new resources for evolutionary studies in Fabales and improves our general understanding of mitogenome evolution. Results Features of the Suriana maritima mitogenome In total, 5.6 Gb of Illumina reads and 43.31 Gb of nanopore clean reads were generated. The average read length of nanopore was 29,915 bp, the read N50 was 36,836 bp, and the longest read was 227,816 bp. The mitogenome of Suriana maritima contained a circular contig with 458,738 bp in length, including 39 protein-coding genes, 20 transfer RNA (tRNA) genes, and three ribosomal RNA (rRNA) genes (Fig. 1 ). The average GC content of the S. maritima mitogenome was 43.5%. The mitogenome contained 24 core and 15 variable genes (Table 1 ). Ten genes contained introns, among which cox1 , rpl2 , rps3 , and ccmFc had one intron; cox2 had two introns; nad4 had three introns; and nad1 , nad2 , nad5 , and nad7 had four introns respectively (Table 1 ). Table 1 Composition of the mitogenome of Suriana maritima Group of genes Genes ATP synthase atp1 , atp4 , atp6 , atp8 , atp9 Cytochrome C biogenesis ccmB , ccmC , ccmFc* , ccmFn Ubichinol Cytochrome C reductase cob Cytochrome C oxidase cox1* , cox2** , cox3 Maturases matR Transport membrane protein mttB NADH dehydrogenase nad1**** , nad2**** , nad3 , nad4*** , nad4L , nad5**** , nad6 , nad7**** , nad9 Large subunit of ribosome rpl2* , rpl5 , rpl10 , rpl16 Small subunit of ribosome rps1 , rps3* , rps4 , rps7 , rps10 , rps12 , rps13 , rps14 , rps19 Succinate dehydrogenase sdh3 , sdh4 Ribosomal RNAs rrn5 , rrn18 , rrn26 Transfer RNA trnC-GCA , trnD-GUC , trnE-UUC , trnF-GAA , trnfM-CAU , trnG-GCC , trnH-GUG , trnI-CAU , trnK-UUU , trnL-CAA , trnM-CAU , trnN-GUU , trnP-UGG , trnQ-UUG , trnS-GCU , trnS-GGA , trnS-UGA , trnV-GAC , trnW-CCA , trnY-GUA Note : Gene* indicates that the gene had intron, * indicates the number of introns Repeat sequence analysis Simple sequence repeats (SSRs), known as microsatellite sequences, are tandem repeats, consisting of several nucleotides (usually 1–6) up to several tens of nucleotides [ 15 ]. A total of 318 SSR sequences were identified in the mitogenome of S. maritima . Mononucleotide A/T repeats were the most prevalent with 199 mononucleotide repeats accounting for 63% of the total SSRs. Additionally, 32 dinucleotide repeats, accounted for 10% of the total SSRs, while trinucleotide and hexanucleotide repeats were less numerous and occurred only in intergenic or intronic regions. There were 16 trinucleotide repeats, 56 tetranucleotide repeats, 56 tetranucleotide repeats, 11 pentanucleotide repeats and 4 hexanucleotide repeats, accounting for 5%, 18%, 3% and 1% of the total SSRs, respectively (Fig. 2 ). Repeats of each base in SSRs (Fig. 3 ) were also counted. A and T repeats were the most frequent, appearing 86 times, followed by C (15 times), G (12 times), and AT (10 times). TA and AT had similar counts (11). Repetitions of the remaining base were all below 5, and there were 69 types of base repeats, and A and T repeated 8 times was frequently detected. There were two types of dispersed repeats in the mitogenome, forward repeats (28) and palindrome repeats (22). Thirty-three long tandem repeats (LTRs), were identified in the mitogenome of Suriana maritima (Table S1). The size of these tandem repeat units, which ranged from 5 bp to 27 bp in length. The longest duplicate unit was 114 bp (13,865–13,979), the shortest was only 26 bp (414,564–414,590). Codon usage bias The codon usage statistics for protein-coding genes (PCGs) are shown in Table 5. A total of 10,963 codons are used for 39 PCGs in the mitogenome of Suriana maritima . There exist AT mutation bias in the coding genes given that the base A and T were used in high frequency in the third-codon position compared to other bases (C v.s. G). The most frequent codon was UUU (Phe), which appeared 403 times, followed by AAA (Lys) with 293 times. The least used CGC encoding arginine (Arg) appeared 65 times, followed by GGC encoding glycine (Gly) (79 times). The three stop codons UAA, UGA, and UAG were recorded 158, 181, and 207 times in the whole mitogenome, respectively, demonstrating a preference for UAG. The Relative synonymous codon usage (RSCU) is usually used to describe the codon usage preferences of each amino acid. RSCU was visually evaluated using ggplot2 [ 16 ] in R, as shown in Table S2 and Fig. 4 . The codons for methionine (Met), tryptophan (Trp), serine (Ser), and arginine (Arg) showed no preference (RSCU = 1). Their codon counterparts are AUG (also the start codon), UGG, UCC, and CGG. There were 29 codons with RSCU > 1 (including a termination codon UAG), indicating a preference for these codons (Fig. 4 and Table S2). For example, arginine had a strong preference for AGA (RSCU = 1.49) and glycine for GGA (RSCU = 1.44). Gene transfer between mitochondrial and plastid genomes Using BLAST v2.10.1 to screen fragments of the mitogenome and plastid genomes of Suriana. maritima showing over 80% identity and performed a homology analysis [ 17 ]. we found tremendous genetic residues of plastids in the mitogenome, which means that sequence transfer is quite common between the two organelle genomes. We identified a total of 83 homologous sequences (Table S3), of which 30 were longer than 1000 bp and the longest was 4379 bp. As determined using TBtools [ 18 ] (Fig. 5 ), we detected substantial collinearity between fragments on mitochondria and plastids. Using the plastid genome as a reference for annotation and found identified 41 plastid genes in mitochondria (Table S4), including 28 CDS and 13 tRNA, with a total of 30,834 bp of homologous sequences. The homologous sequences accounted for 18.8% of the plastid genome and 6.7% of the mitogenome, indicating that the plastid genome of Suriana maritima is a rich source of foreign sequences in the mitogenome. In particular, 16 plastid genes ( ycf3 , psaA, psaB , matK , atpB , atpI , rps2 , rps4 , atpF , rps7 , rpl23 , atpH , petN , trnC-GCA , trnI-CAU , and trnS - GGA ) have been completely transferred into the mitogenome (Fig. 6 ). Mapping the 29 genes transferred from the plastids to mitochondria with the transcriptome data, 20 genes can distinguish between mitochondria and plastid genome, the highest expression is in 24 transcripts, and the average expression of normal plastid genes and mitochondrial genes is 100, so it is assumed that the expression of the genes that have been transferred is low (Table S7). Discussion Assembly of a high-quality mitogenome of Suriana maritima Compared with plastid genome assembly, the assembly of the mitochondrial genome is more difficult. Firstly, there is no effective method to enrich plant mitochondria before DNA extraction [ 19 ]. Second, the mitochondrial structure is extremely diverse, and the plant mitogenome shows substantial variation in size, with frequent structural rearrangements, even within closely related species [ 20 , 21 ]. For example, in the family Cucurbitaceae, the mitogenome of Citrullus lanatus is 379 kb [ 20 ], while that of Cucumis sativus is 2.74 Mb [ 22 ], which is seven times the size of the former. Even greater variation has been detected within the genus Silene , with estimates ranging from 253 kb to 11 Mb [ 23 ]. Several technical limitations using the data of second genome sequencing may affect the quality of mitogenome assembly as well. Therefore, it is challenging to ascertain whether an assembly is complete or not. In this study the mitogenome was assembled from total DNAs with a hybrid assembly strategy, combining the unitig sequences assembled from short Illumina reads and contigs assembled from long Nanopore reads. This strategy can avoid false positives caused by the polishing strategy. During assembly of the S. maritima mitogenome, the depth at several sites determined by mapping to Illumina reads was relatively low (data not shown). This may be explained by assembly errors or may reflect differences among tissue types, as has been found in other plant species (Fig. 7 ).We thus performed error correction with the second-generation data (Fig. 8 ); for two loci with low depth we used PCR and Sanger sequencing to obtain a high-quality mitogenome. We obtained the first complete mitogenome for S. maritima in Suriana (family Surianaceae), which is expected to provide a useful reference for follow-up studies of the function and structure of plant mitochondria. Bioinformatic predictions must be further validated by quantitative PCR experiments, Sanger sequencing, Southern blot, and electronic microscopy [ 24 , 25 ]. Structural characteristics of the Suriana maritima mitogenome The mitogenome of S. maritima is a circular structure (Fig. 1 ). The structure of plant mitogenomes shows great instability [ 26 ], and various structures have been reported, including linear, branching, and polychromosomal structures. The mitogenome of the garden rocket contains six main ring structures and four small subring molecules, which may be due to the complex structure of the repetitive sequences [ 27 ]. A multichromosomal mitogenome structure has been verified in various angiosperms, including Cucumis sativus , Silene gallica , Amborella trichopoda , and parasitic plants [ 5 , 28 – 30 ]. However, the typical mitogenome structure consists of ring molecules [ 31 ], as observed in Leucaena trichandra [ 32 ], and Dalbergia odorifera [ 9 ]. Repeat sequence-mediated homologous recombination is universal in plant mitogenomes [ 33 , 34 ]. The large number of repeats (> 1000 bp) may lead to a more complex structure, which can also explain why there are fewer genes in the mitogenome than the plastid genome, despite its much larger length. In the assembly of the S. maritima mitogenome, we also identified repetitive sequences suggesting substantial recombination (Fig. 2 ). Plant mitogenomes are rich in repetitive sequences, accounting for up to 38% of the genome size [ 26 ]; however, the origin of repetitive sequences remains unclear. There were 318 simple repeats, 33 long tandem repeats, and 50 dispersed repeats in S. maritima (Fig. 2 , Table S1). Based on plant mitogenome sequences available to data, the content and composition of plant mitochondrial repeat sequences differ substantially[ 35 ], indicating that these sequences were obtained independently during evolution [ 36 ]. Therefore, repeated sequences in the plant mitogenome are closely related to recombination [ 31 ], resulting in a highly complex plant mitochondrial structure and causing male abortion in plants. Mitochondrial functional genes are highly conserved [ 37 ], and the majority of genomic variation is found in intergenic regions [ 38 ]. Intergenic sequences are characterized by a large number of repeated sequences and imported sequences [ 30 ] as well as intron length variation and pseudogene factors [ 39 ]. Repetitive sequences appear in highly variable intergenic regions [ 31 ], frequent structural rearrangements [ 40 ], substantial gene loss, and the transfer of endogenous and exogenous DNA [ 41 ], The long repeats in the mitogenome also had a high frequency of recombination. Short repeats had a low recombination frequency, consistent with previous results [ 42 ]. In addition, mitochondrial PCGs have strong codon preference. UUU encoding phenylalanine (Phe) is the most frequently used codon, while the CGC encoding arginine (Arg) is the least codon in the PCGs in the mitogenomes of S. maritima . Gene transfer between mitochondria and plastid genomes Genes transferred from the plastid genome are commonly found in plant mitogenomes, typically representing 1–12% of the total length [ 43 ]. In contrast, the transfer of sequences from the plant mitogenome into plastid genomes is nearly impossible, since the plastid genome is relatively conserved and does not accept the integration of foreign DNA fragments [ 44 ]. The transfer of plastid DNA to the mitogenome occurred at least 300 million years ago [ 45 ]. No insertions of plastid and nuclear genes were found in the mitogenome of bryophytes, indicating that the absorption of foreign DNA by plant mitochondria occurred during the evolution of vascular plants [ 46 ]. Compared with previous studies of other taxa, the mitogenome of S. maritima had the highest rates of transfer from the plastid genome. Homologous sequences with a total length of 30,834 bp accounted for 18.8% of the plastid genome and 6.7% of the mitogenome of S. maritima (Table S3). The smaller mitogenome of Citrullus lanatus contains about 23 kb of transferred plastid sequences. More 5% of the mitogenomes of Cucurbita pepo is derived from plastid sequences of (approximately 113 kb) [ 47 ]. Plastid-to-mitochondrion sequences are 1.67 kb in Silene and 3.52 kb in Vigna radiata [ 7 ]. In Bupleurum chinense , the total length of sequences transferred from the plastid genome to the mitogenome was found to be 11,144 bp, accounting for 2.56% of the mitogenome [ 8 ]. Early studies have shown that plastid-derived tRNA genes are required for the translation of plant mitogenomes [ 23 ]. The plastid fragments that were transferred to mitochondria mostly include genes, pseudogenes, and intergenomic sequences [ 3 ]. Most functional genes are tRNA genes, while other genes are generally not expressed and many become pseudogenes gradually over time [ 48 , 49 ]. Here, we identified 16 full-length genes that have been completely transferred from the plastid of S. maritima to the mitogenome (i.e., ycf3 , psaA, psaB , matK , atpB , atpI , rps2 , rps4 , atpF , rps7 , rpl23 , atpH , petN , trnC-GCA , trnI-CAU , and trnS - GGA ) (Fig. 6 ). However, these genes might not function in mitochondria, and they might undergo pseudogenization [ 50 ]. Pseudogenes mainly encode important proteins; however, complete plastid protein genes have also been found in Vitis vinifera [ 51 ]. For example, the rpl32 gene from the plastid has been transferred into in the subfamily Thalictroideae (family Ranunculaceae)[ 52 ]. Three complete genes in the mitogenomes migrated from the plastid genome of okra, including psaA , rps7 , and psbJ , in addition to several plastid-derived gene fragments [ 53 ]. In addition, we found that S. maritima has substantial differences in fragment position caused by the insertion of plastid genes into the mitogenome. Intracellular gene transfer may be responsible for the high degree of rearrangement [ 54 ]. Since the plastid genome fragments are well-aligned with the original plastid genome sequence, this gene transfer may cause the disassembly of the mitogenome. The mitochondrial and nuclear genomes can transfer DNA sequences in both directions. However, most studies have found that plastid genome fragments are only transferred to the nuclear and mitogenomes, while other genomes are not transferred to the plastid, and the plastid genome tends not to integrate foreign DNA [ 55 , 56 ]. Conclusions In this study, we successfully assembled the mitogenome of S. maritima with a high quality by using both Nanopore and Illumina reads, enabling a comprehensive comparison of the organelle genomes of S. maritima . A single circular master molecule represents the mitogenome of S. maritima . The chloroplast genome of S. maritima provided abundant foreign sequences in the mitogenome, including 41 plastid genes among 83 mitochondrial plastid DNA sequences with a total length of 30,834 bp. The transferred sequences accounted for 18.8% of the plastid genome and 6.7% of the mitogenome, which is much higher than previous estimates in Fabales. This study provided strong evidence for gene transfer between the mitochondria and plastids genes. Additional sampling from all families in the order are needed to more fully understand their complex history and the functional interplay between plastid and mitochondrial genetics. Materials and methods Taxon sampling, DNA extraction and sequencing We collected S. maritima in Xisha Islands (China) and cultivated plants at the South China Botanical Garden, CAS. Total genomic DNA was extracted from fresh leaves using a modified cetyltrimethylammonium bromide (CTAB) method [ 57 ]. Second-generation sequencing was conducted using the Illumina HiSeq-2500 platform with a read length of 150 bp. Sequencing produced a total of 5.6 Gb of raw data. For Oxford Nanopore sequencing, purified DNA was prepared for long-read sequencing following the protocol provided with the SQK-LSK109 genomic sequencing kit (Oxford Nanopore Technologies, Oxford, UK). Extraction, database constuction, and sequencing were completed by Beijing Baimaike Biotechnology Co., Ltd.]\ Mitogenome assembly We initially assembled the mitogenome of S. maritima using Illumina short reads. GetOrganelle v1.7.7.0 was used for assembly with the parameter setting “embplant_mt” and a custom mitochondrial database as references [ 58 ]. The output contained 238 contigs of 276–89,145 bp in length, with a total length of 637,303 bp. When visualizing the raw GFA file produced by GetOrganelle in Bandage v0.8.1 [ 59 ], the mitogenome consisted of a network of connected contigs (Figure S1). Unnecessary contigs were manually deleted. After many rounds of verification, a complete closed-loop structure was obtained. The published mitochondrial CDS sequences of Leucaena trichandra and Vicia faba were used as references (among which Leucaena trichandra contained 56 CDS sequences and Vicia faba contained 61 CDS sequences). Minimap2 [ 60 ] was used to identify putative mitochondrial Nanopore reads of S. maritima . Then, Canu [ 61 ] to perform self-correction and trimming of the identified putative mitochondrial Nanopore reads. The parameters are set to: genomeSize = 2m, corThreads = 64; For the assembly result, LoRDEC [ 62 ] was used to correct the reads twice and trim once, with the following parameter settings: -k = 19, -s = 3; The parameters for retrimming and assembly were genomeSize = 2m, minReadLength = 5000, and correctedErrorRate = 0.134 to obtain 11 contigs with lengths of 26,663–514,650 bp (Table S5). The Canu assembly result showed that contig1 was"suggestCircular." Considering that the length of this contig was the longest among the 11 contigs, it might represent the true mitogenome sequence of S. maritima . To further verify whether contig1 is a complete mitogenome, Illumina reads (5.6 Gb) were mapped to the 41 genes (24 core genes and 17 variable genes) of angiosperm mitogenomes using Bowtie2 [ 63 ], and the mapped reads were extracted using Samtools v1.9 [ 64 ] with the parameter -bF 4, generating a much smaller subset of Illumina mitochondrial reads. We then calculated their depth of coverage using Samtools. It was found that 39 genes had a depth of coverage of > 5000×, except rps2 and rps11 (2–16 for rps2 and rps11 ) (Table S6). These 39 genes except rps2 and rps11 exist in the mitogenome of S. maritima . The above 39 genes were used as a reference genome to annotate contig1, revealing that contig1 contained 39 genes except for rps2 and rps11 . Therefore, contig1 may contain the complete information of the mitogenome of S. maritima . Then, Pilon [ 65 ] was used for gap filling and sequence correction with default settings until its depth reached 5000–8000, and this was used in subsequent analyses. Genome annotation The web-based tool Public MITOFY Analysis was used to identify genes [ 20 ]. We also revised the start and stop codons of genes based on similar genes, manually checked by MITOFY against other sequenced mitogenomes. Mitogenome annotation was performed using the BLASTN alignment tools of the National Center for Biotechnology Information (NCBI) database ( https://www.ncbi.nlm.nih.gov/ ) with the gene bank of angiosperm mitogenomes as reference sequences. The tRNAs were annotated using tRNAscan-SE [ 66 ] with default settings. The circular mitogenome map was drawn using OGDRAW [ 67 ]. The final mitogenome of S. maritima has been deposited in GenBank (Accession number: OQ933798). Analysis of mitogenome characteristics The GC content was determined using the cusp program provided by EMBOSS [ 68 ]. The SSRs of the mitogenome of S. maritima were analyzed using Misa [ 69 ] ( https://webblast.ipk-gatersleben.de/misa/ ), with a size of one to six nucleotides, thresholds of eight, five, four, three, three, and three, separately, and a minimum distance between two SSRs of 100 bp. REPuter [ 70 , 71 ] ( https://bibiserv.cebitec.uni-bielefeld.de/reputer/ ) was used to calculate palindromic repeats, forward repeats, reverse repeats, and complement repeats with the following settings: hamming distance of three and minimal repeat size of 30 bp. LTR identification was performed using the "Advanced" module of Tandem Repeats Finder [ 72 ] ( https://tandem.bu.edu/trf/trf.html ) with default settings. Codon preference (synonymous codon usage, RSCU) of mitochondrial PCGs of the S. maritima mitogenome was calculated using CodonW. Identification of plastid gene transfer to the mitogenome The complete plastids genome of S. maritima (NC_047313.1) [ 73 , 74 ] was downloaded from the NCBI Organelle Genome Resources database. Plastid gene transfer to the mitogenome were identified using BLAST [ 75 ], with the following parameter settings:- evalue 1e-5, -word_size 9, -gapopen 5, -gapextend 2, -reward 2, -penalty-3, and -dust no [ 42 ]. Screening criteria were set with an identity threshold of ≥ 80%. The identification results were visualized with reference to collinearity analysis uusing the "Advanced Circos" module of TBtools [ 18 ]. Abbreviations PCG Protein-coding genes tRNA Transfer RNA rRNA Ribosomal RNA Mitogenome Mitochondrial genome NCBI National Center for Biotechnology Information SSR Simple sequence repeat BLAST Basic Local Alignment Search Tool LTR Long tandem repeats RSCU Relative Synonymous Codon Usage CDS:Coding sequence. Declarations Ethics approval and consent to participate The material involved in the article does not involve ethical conflicts. Field studies complied with local legislation, and appropriate permissions were granted before the samples were collected from the South China Botanical Garden. Consent for publication Not applicable. Competing interests The authors declare that they have no competing interests. Availability of data and materials The complete mitogenome sequence of Suriana. maritima has been deposited in the GenBank database under the accession number OQ933798 (these numbers were automatically generated by NCBI and refer to the same sample). The associated BioProject, SRA, and Bio-Sample numbers are PRJxxxxx, SRRxxxx, and SAMNxxxxx, respectively. Funding This work was financially supported by the National Natural Science Foundation of China (32070222, 32170232), the National Key Research and Development Program of China (2021YFC3100405) and the Guangdong Provincial Special Fund for Natural Resource Affairs on Ecology and Forestry Construction (GDZZDC20228704). Authors' contributions In this research, Jian-Xin Li conceived and designed the study. She has completed the data analysis and the first draft of the paper. 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Doyle, A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochemical Bulletin, 1987. 19(1): p. 11-15. Jin, J.J., et al., GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes. Genome Biology, 2020. 21(1): p. 241. Wick, R.R., et al., Bandage: interactive visualization of de novo genome assemblies. Bioinformatics , 2015. 31(20): p. 3350-3352. Li, H., Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics, 2018. 34(18): p. 3094-3100. Koren, S., et al., Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation. Genome Research, 2017. 27(5): p. 722-736. Salmela, L. and E. Rivals, LoRDEC: accurate and efficient long read error correction. Bioinformatics, 2014. 30(24): p. 3506-14. Langmead, B. and S.L. Salzberg, Fast gapped-read alignment with Bowtie 2. Nature Methods, 2012. 9(4): p. 357-359. Danecek, P., et al., Twelve years of SAMtools and BCFtools. Gigascience, 2021. 10(2). Walker, B.J., et al., Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One, 2014. 9(11): p. e112963. Chan, P.P. and T.M. Lowe, tRNAscan-SE: searching for tRNA genes in genomic sequences. Methods in Molecular Biology, 2019. 1962: p. 1-14. Greiner, S., P. Lehwark, and R. Bock, OrganellarGenomeDRAW (OGDRAW) version 1.3.1: expanded toolkit for the graphical visualization of organellar genomes. Nucleic Acids Research, 2019: p. 545509. Rice P, L.I., Bleasby A. , EMBOSS the european molecular biology open software suite Trends Genet, 2000. 16: p. 276-7. Beier, S., et al., MISA-web: a web server for microsatellite prediction. Bioinformatics, 2017. 33(16): p. 2583-2585. Kurtz S, S.C., REPuter fast computation of maximal repeats in complete genomes. Bioinformatics, 1999. 15: p. 426-7. Kurtz S, C.J., Ohlebusch E, Schleiermacher C, Stoye J, Giegerich R., REPuter the manifold applications of repeat analysis on a genomic scale. Nucleic Acids Research, 2001. 29(22): p. 4633-42. G., B., Tandem repeats finder a program to analyze DNA sequences. Nucleic Acids Research, 1999. 27: p. 573-80. Lai, Q., et al., Complete plastid genome of Suriana maritima L. (Surianaceae) and its implications in phylogenetic reconstruction of Fabales. Journal of Genetics, 2019. 98(5). Zhang, R., et al., Exploration of Plastid Phylogenomic Conflict Yields New Insights into the Deep Relationships of Leguminosae. Systematic Biology, 2020. Johnson, M., et al., NCBI BLAST: a better web interface. Nucleic Acids Res, 2008. 36(Web Server issue): p. W5-9. Additional Declarations No competing interests reported. Supplementary Files SuppTable.docx FigureS1Structurediagramofthesecond.docx Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-3948491","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":272273482,"identity":"ccd5e30d-c477-452a-8707-3a920f57da72","order_by":0,"name":"Jian-Xin Li","email":"","orcid":"","institution":"Jishou University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Jian-Xin","middleName":"","lastName":"Li","suffix":""},{"id":272273483,"identity":"af5f47b2-15ff-401a-b17b-d3e71c575933","order_by":1,"name":"Runxian Yu","email":"","orcid":"","institution":"University of Chinese Academy of Sciences","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Runxian","middleName":"","lastName":"Yu","suffix":""},{"id":272273484,"identity":"6be39463-7b2c-4612-a578-a4367a10dc76","order_by":2,"name":"Ze-Long Nie","email":"","orcid":"","institution":"Jishou University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Ze-Long","middleName":"","lastName":"Nie","suffix":""},{"id":272273485,"identity":"bffbb6ad-38f6-4478-8838-436be5255920","order_by":3,"name":"Meng hua Zhang","email":"","orcid":"","institution":"Jishou University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Meng","middleName":"hua","lastName":"Zhang","suffix":""},{"id":272273486,"identity":"600b360d-d6eb-40fd-a3e2-c460d4df9414","order_by":4,"name":"Miao-Miao Shi","email":"","orcid":"","institution":"Chinese Academy of Sciences","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Miao-Miao","middleName":"","lastName":"Shi","suffix":""},{"id":272273487,"identity":"08799648-d514-4582-b015-54b51da6de29","order_by":5,"name":"Zhongtao Zhao","email":"","orcid":"","institution":"Chinese Academy of Sciences","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Zhongtao","middleName":"","lastName":"Zhao","suffix":""},{"id":272273488,"identity":"0cf2dd38-5327-4dcf-8418-8348a9d09c96","order_by":6,"name":"Shijin Li","email":"","orcid":"","institution":"Chinese Academy of Sciences","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Shijin","middleName":"","lastName":"Li","suffix":""},{"id":272273489,"identity":"e09b2e54-d264-4100-a38c-9716ab6102ee","order_by":7,"name":"Xiang-Ping Wang","email":"","orcid":"","institution":"Chinese Academy of Sciences","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Xiang-Ping","middleName":"","lastName":"Wang","suffix":""},{"id":272273490,"identity":"e7beafb0-27a6-4047-b2ea-c00d4770ce4c","order_by":8,"name":"Ying Meng","email":"","orcid":"","institution":"Jishou University","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Ying","middleName":"","lastName":"Meng","suffix":""},{"id":272273491,"identity":"c39f96f8-0ba5-423b-b65f-dc6ed466ffdb","order_by":9,"name":"Tieyao Tu","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAA0ElEQVRIiWNgGAWjYJCCAyCCn4GBjTjlPAzMEC2SDaRoAQODA8RqsZfIP3jgY5udnPH5w88efmGwk2dgP3sAvy0SyQwHZ7YlG5vdSDM3lmFINmzgyUsgqOUwbxtz4rYbPGzSEgzMCQwSPAaEtfxtq0/c3H8GpKWeSC2MbYcTNzDksEl+YDhMhJYzjw0O9pw7biwB8guDwXHDNp4c/FrY2xMff/hRVi3H3w8MsR8V1fL87GfwawEDRmiMMIOcRGTs/IFq/UGc8lEwCkbBKBhhAACQ7j2mcaenxgAAAABJRU5ErkJggg==","orcid":"","institution":"Chinese Academy of Sciences","correspondingAuthor":true,"submittingAuthor":false,"prefix":"","firstName":"Tieyao","middleName":"","lastName":"Tu","suffix":""},{"id":272273492,"identity":"55f7749d-7d51-4373-9384-1076a4979470","order_by":10,"name":"Dianxiang Zhang","email":"","orcid":"","institution":"Chinese Academy of Sciences","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Dianxiang","middleName":"","lastName":"Zhang","suffix":""}],"badges":[],"createdAt":"2024-02-11 12:59:34","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-3948491/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-3948491/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":51382000,"identity":"9d92c4ed-18eb-4246-b54f-6e879b836472","added_by":"auto","created_at":"2024-02-20 16:12:39","extension":"png","order_by":1,"title":"Figure 1","display":"","copyAsset":false,"role":"figure","size":137310,"visible":true,"origin":"","legend":"\u003cp\u003eMitogenome map of \u003cem\u003eSuriana maritima\u003c/em\u003e. Genes in the circle are transcribed clockwise and genes outside the circle are transcribed counterclockwise. Genes belonging to different functional groups are color-coded. The darker gray area in the inner ring corresponds to GC content, while the lighter gray area corresponds to AT content.\u003c/p\u003e","description":"","filename":"1.png","url":"https://assets-eu.researchsquare.com/files/rs-3948491/v1/f2008c7d3483d9faf2d7457a.png"},{"id":51381410,"identity":"285989ab-34a6-4545-8f52-ed7e44a0d234","added_by":"auto","created_at":"2024-02-20 16:04:39","extension":"png","order_by":2,"title":"Figure 2","display":"","copyAsset":false,"role":"figure","size":85297,"visible":true,"origin":"","legend":"\u003cp\u003eProportions of simple sequence repeats (SSRs) types in the mitogenome of \u003cem\u003eSuriana maritima.\u003c/em\u003e\u003c/p\u003e","description":"","filename":"2.png","url":"https://assets-eu.researchsquare.com/files/rs-3948491/v1/69e6b5d9b617789936ee7792.png"},{"id":51381412,"identity":"bb5739c6-bc67-4285-aa22-7f567e950fed","added_by":"auto","created_at":"2024-02-20 16:04:39","extension":"png","order_by":3,"title":"Figure 3","display":"","copyAsset":false,"role":"figure","size":62692,"visible":true,"origin":"","legend":"\u003cp\u003eComparison of mitochondrial SSRs repeat units in the mitogenome of \u003cem\u003eSuriana maritima.\u003c/em\u003e\u003c/p\u003e","description":"","filename":"3.png","url":"https://assets-eu.researchsquare.com/files/rs-3948491/v1/900bfdf5c2dbf5c892971411.png"},{"id":51381415,"identity":"6d39ad71-58d8-4ba1-b146-5739f38e24f6","added_by":"auto","created_at":"2024-02-20 16:04:39","extension":"png","order_by":4,"title":"Figure 4","display":"","copyAsset":false,"role":"figure","size":98156,"visible":true,"origin":"","legend":"\u003cp\u003eCodon usage preferences for mitochondrial PCGs in \u003cem\u003eSuriana maritima\u003c/em\u003e\u003c/p\u003e","description":"","filename":"4.png","url":"https://assets-eu.researchsquare.com/files/rs-3948491/v1/1a7008a5c55a5615a25e594f.png"},{"id":51381414,"identity":"b3e70f9a-8057-490e-8b44-47d36691a233","added_by":"auto","created_at":"2024-02-20 16:04:39","extension":"png","order_by":5,"title":"Figure 5","display":"","copyAsset":false,"role":"figure","size":693794,"visible":true,"origin":"","legend":"\u003cp\u003eVisualization of Blastn results for the mitogenome and plastid genome of \u003cem\u003eSuriana maritima.\u003c/em\u003e\u003c/p\u003e","description":"","filename":"5.png","url":"https://assets-eu.researchsquare.com/files/rs-3948491/v1/36bafccc6b7441ae785bfaa5.png"},{"id":51381418,"identity":"497c14f3-3861-4bc4-a2e5-4ddff9928bb9","added_by":"auto","created_at":"2024-02-20 16:04:39","extension":"png","order_by":6,"title":"Figure 6","display":"","copyAsset":false,"role":"figure","size":140258,"visible":true,"origin":"","legend":"\u003cp\u003eGenes transferred from the plastid genome to the mitogenome.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eNote\u003c/strong\u003e：1–42 represent \u003cem\u003eatpB, atpE\u003c/em\u003e, \u003cem\u003eatpF\u003c/em\u003e, \u003cem\u003eatpH\u003c/em\u003e, \u003cem\u003eatpI\u003c/em\u003e, \u003cem\u003endhB\u003c/em\u003e, \u003cem\u003ematK\u003c/em\u003e, \u003cem\u003epetG\u003c/em\u003e, \u003cem\u003epetL\u003c/em\u003e, \u003cem\u003epetN\u003c/em\u003e, \u003cem\u003epsaA\u003c/em\u003e, \u003cem\u003epsbB\u003c/em\u003e, \u003cem\u003epsbC\u003c/em\u003e, \u003cem\u003epsbD\u003c/em\u003e, \u003cem\u003epsbZ\u003c/em\u003e, \u003cem\u003erbcL\u003c/em\u003e, \u003cem\u003erpl14\u003c/em\u003e, \u003cem\u003erpl2\u003c/em\u003e, \u003cem\u003erpl22\u003c/em\u003e, \u003cem\u003erpl23\u003c/em\u003e, \u003cem\u003erps2\u003c/em\u003e, \u003cem\u003erps3\u003c/em\u003e, \u003cem\u003erps4\u003c/em\u003e, \u003cem\u003erps7\u003c/em\u003e, \u003cem\u003erps14\u003c/em\u003e, \u003cem\u003eycf3\u003c/em\u003e, \u003cem\u003etrnD-GUC\u003c/em\u003e, \u003cem\u003etrnH-GUG\u003c/em\u003e, \u003cem\u003etrnM-CAU\u003c/em\u003e, \u003cem\u003etrnN-GUU\u003c/em\u003e, \u003cem\u003etrnW-CCA\u003c/em\u003e, \u003cem\u003etrnI-CAU\u003c/em\u003e, \u003cem\u003etrnP-UGG\u003c/em\u003e, \u003cem\u003etrnV-GAC\u003c/em\u003e, \u003cem\u003etrnA-UGC\u003c/em\u003e, \u003cem\u003etrnS-GGA\u003c/em\u003e, \u003cem\u003etrnC-GCA\u003c/em\u003e, \u003cem\u003etrnfM-CAU\u003c/em\u003e, \u003cem\u003etrnG-GCC\u003c/em\u003e, \u003cem\u003etrnK-UUU\u003c/em\u003e, \u003cem\u003etrnL-CAA\u003c/em\u003e, and \u003cem\u003etrnT-GGU\u003c/em\u003e\u003c/p\u003e","description":"","filename":"6.png","url":"https://assets-eu.researchsquare.com/files/rs-3948491/v1/83ff94cad83ec09e0bb5bff6.png"},{"id":51381419,"identity":"aa931cf6-62a1-43b7-92cc-e6342691fdcd","added_by":"auto","created_at":"2024-02-20 16:04:39","extension":"png","order_by":7,"title":"Figure 7","display":"","copyAsset":false,"role":"figure","size":63974,"visible":true,"origin":"","legend":"\u003cp\u003eDepth of coverage of Illumina reads along the Nanopore assembly.\u003c/p\u003e","description":"","filename":"7.png","url":"https://assets-eu.researchsquare.com/files/rs-3948491/v1/b67ae4392f809f0e5897220c.png"},{"id":51381417,"identity":"baeaa187-3b90-4420-9348-6a17bd73b34d","added_by":"auto","created_at":"2024-02-20 16:04:39","extension":"png","order_by":8,"title":"Figure 8","display":"","copyAsset":false,"role":"figure","size":53622,"visible":true,"origin":"","legend":"\u003cp\u003eDepth of coverage of Illumina reads along the corrected Nanopore assembly.\u003c/p\u003e","description":"","filename":"8.png","url":"https://assets-eu.researchsquare.com/files/rs-3948491/v1/97e90d4f24d5c367a5c22e7a.png"},{"id":58499231,"identity":"5b2ca584-69cd-4c16-bc7f-635cbac3b3a4","added_by":"auto","created_at":"2024-06-17 12:59:31","extension":"pdf","order_by":0,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":2000476,"visible":true,"origin":"","legend":"","description":"","filename":"manuscript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-3948491/v1/436ba0db-d32e-4389-b661-fd5ab41ca54b.pdf"},{"id":51381409,"identity":"8fff2e70-2ae7-4e7e-8b83-b2e0ed09083c","added_by":"auto","created_at":"2024-02-20 16:04:38","extension":"docx","order_by":1,"title":"","display":"","copyAsset":false,"role":"supplement","size":67569,"visible":true,"origin":"","legend":"","description":"","filename":"SuppTable.docx","url":"https://assets-eu.researchsquare.com/files/rs-3948491/v1/7d34264a0e674a4467796bc8.docx"},{"id":51381413,"identity":"8aead119-fdfb-442c-91ce-1f8e4f9e4266","added_by":"auto","created_at":"2024-02-20 16:04:39","extension":"docx","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":545645,"visible":true,"origin":"","legend":"","description":"","filename":"FigureS1Structurediagramofthesecond.docx","url":"https://assets-eu.researchsquare.com/files/rs-3948491/v1/b92336643a8ceac8232e8508.docx"}],"financialInterests":"No competing interests reported.","formattedTitle":"A high-quality mitochondrial genome of Suriana maritima reveals tremendous gene transfers between the plastid and mitochondrial genomes","fulltext":[{"header":"Background","content":"\u003cp\u003eThe plant mitogenome is mainly assembled into a circular structure containing all genes [\u003cspan citationid=\"CR1\" class=\"CitationRef\"\u003e1\u003c/span\u003e], generally known as the \u0026ldquo;master circle\u0026rdquo;, with a few exceptions as linear, branched, overlapping, or multiple coexisting structures [\u003cspan additionalcitationids=\"CR3 CR4\" citationid=\"CR2\" class=\"CitationRef\"\u003e2\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e]. Redundant sequences and extensive genomic recombination make it difficult to recover the conformation of the plant mitogenome. In particular, it is difficult to correctly assemble the mitogenome based on second-generation sequencing data and accurately evaluate mitogenome evolution, including codon usage, RNA editing, horizontal transfer, gene loss and acquisition [\u003cspan citationid=\"CR6\" class=\"CitationRef\"\u003e6\u003c/span\u003e]. Among these, intracellular gene transfer has been found in several lineages of plants. For example, the genome transferred from plastid to mitochondrion span 1.67 kb in \u003cem\u003eSilene\u003c/em\u003e (Caryophyllaceae) and 3.52 kb in \u003cem\u003eVigna radiata\u003c/em\u003e(Fabaceae) [\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e]. The total length of \u003cem\u003eBupleurum chinense\u003c/em\u003e (Apiaceae) sequence transferred from the plastid genome to the mitogenome is 11,144 bp, accounting for 2.56% of the mitogenome [\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e]. However, analyses of gene transfer between the plastid, mitochondrial, or nuclear genomes in a broader range of taxa are needed, including species closely related to legumes are lacking.\u003c/p\u003e \u003cp\u003eFabales contains four families, namely Leguminosae, Polygallaceae, Quillajaceae and Surianaceae [\u003cspan citationid=\"CR10\" class=\"CitationRef\"\u003e10\u003c/span\u003e]. Surianaceae is a small family with only five woody genera and eight species distributed in pantropical areas, and, in particular, in Australia and Mexico [\u003cspan citationid=\"CR11\" class=\"CitationRef\"\u003e11\u003c/span\u003e, \u003cspan citationid=\"CR12\" class=\"CitationRef\"\u003e12\u003c/span\u003e]. \u003cem\u003eSuriana maritima\u003c/em\u003e L. is the member of Surianaceae and shows with an extensive distribution in the tropical coral islands and coastal zones. In China, it is only found on the Xisha Islands and Dongsha Islands (coral islands) in the South China Sea, mainly growing on the sandy land or rock cracks, as a pioneer species [\u003cspan citationid=\"CR13\" class=\"CitationRef\"\u003e13\u003c/span\u003e, \u003cspan citationid=\"CR14\" class=\"CitationRef\"\u003e14\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eIn this study, we assembled a high-quality mitogenome of \u003cem\u003eS. maritima\u003c/em\u003e using both Illumina and Nanopore technologies and analyzed its genomic and structural features as well as the role of gene transfer from plastids. This study provides new resources for evolutionary studies in Fabales and improves our general understanding of mitogenome evolution.\u003c/p\u003e"},{"header":"Results","content":"\u003cp\u003e \u003cb\u003eFeatures of the\u003c/b\u003e \u003cb\u003eSuriana maritima\u003c/b\u003e \u003cb\u003emitogenome\u003c/b\u003e\u003c/p\u003e \u003cp\u003eIn total, 5.6 Gb of Illumina reads and 43.31 Gb of nanopore clean reads were generated. The average read length of nanopore was 29,915 bp, the read N50 was 36,836 bp, and the longest read was 227,816 bp. The mitogenome of \u003cem\u003eSuriana maritima\u003c/em\u003e contained a circular contig with 458,738 bp in length, including 39 protein-coding genes, 20 transfer RNA (tRNA) genes, and three ribosomal RNA (rRNA) genes (Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e1\u003c/span\u003e). The average GC content of the \u003cem\u003eS. maritima\u003c/em\u003e mitogenome was 43.5%. The mitogenome contained 24 core and 15 variable genes (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e). Ten genes contained introns, among which \u003cem\u003ecox1\u003c/em\u003e, \u003cem\u003erpl2\u003c/em\u003e, \u003cem\u003erps3\u003c/em\u003e, and \u003cem\u003eccmFc\u003c/em\u003e had one intron; \u003cem\u003ecox2\u003c/em\u003e had two introns; \u003cem\u003enad4\u003c/em\u003e had three introns; and \u003cem\u003enad1\u003c/em\u003e, \u003cem\u003enad2\u003c/em\u003e, \u003cem\u003enad5\u003c/em\u003e, and \u003cem\u003enad7\u003c/em\u003e had four introns respectively (Table\u0026nbsp;\u003cspan refid=\"Tab1\" class=\"InternalRef\"\u003e1\u003c/span\u003e).\u003c/p\u003e \u003cp\u003e \u003cdiv class=\"gridtable\"\u003e\u003ctable float=\"Yes\" id=\"Tab1\" border=\"1\"\u003e \u003ccaption language=\"En\"\u003e \u003cdiv class=\"CaptionNumber\"\u003eTable 1\u003c/div\u003e \u003cdiv class=\"CaptionContent\"\u003e \u003cp\u003eComposition of the mitogenome of \u003cem\u003eSuriana maritima\u003c/em\u003e\u003c/p\u003e \u003c/div\u003e \u003c/caption\u003e \u003ccolgroup cols=\"2\"\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c1\" colnum=\"1\"\u003e\u003c/div\u003e \u003cdiv align=\"left\" class=\"colspec\" colname=\"c2\" colnum=\"2\"\u003e\u003c/div\u003e \u003cthead\u003e \u003ctr\u003e \u003cth align=\"left\" colname=\"c1\"\u003e \u003cp\u003eGroup of genes\u003c/p\u003e \u003c/th\u003e \u003cth align=\"left\" colname=\"c2\"\u003e \u003cp\u003eGenes\u003c/p\u003e \u003c/th\u003e \u003c/tr\u003e \u003c/thead\u003e \u003ctbody\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eATP synthase\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eatp1\u003c/em\u003e, \u003cem\u003eatp4\u003c/em\u003e, \u003cem\u003eatp6\u003c/em\u003e, \u003cem\u003eatp8\u003c/em\u003e, \u003cem\u003eatp9\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCytochrome C biogenesis\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003eccmB\u003c/em\u003e, \u003cem\u003eccmC\u003c/em\u003e, \u003cem\u003eccmFc*\u003c/em\u003e, \u003cem\u003eccmFn\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eUbichinol Cytochrome C reductase\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003ecob\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eCytochrome C oxidase\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003ecox1*\u003c/em\u003e, \u003cem\u003ecox2**\u003c/em\u003e, \u003cem\u003ecox3\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eMaturases\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003ematR\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eTransport membrane protein\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003emttB\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eNADH dehydrogenase\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003enad1****\u003c/em\u003e, \u003cem\u003enad2****\u003c/em\u003e, \u003cem\u003enad3\u003c/em\u003e, \u003cem\u003enad4***\u003c/em\u003e, \u003cem\u003enad4L\u003c/em\u003e, \u003cem\u003enad5****\u003c/em\u003e, \u003cem\u003enad6\u003c/em\u003e, \u003cem\u003enad7****\u003c/em\u003e, \u003cem\u003enad9\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eLarge subunit of ribosome\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003erpl2*\u003c/em\u003e, \u003cem\u003erpl5\u003c/em\u003e, \u003cem\u003erpl10\u003c/em\u003e, \u003cem\u003erpl16\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eSmall subunit of ribosome\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003erps1\u003c/em\u003e, \u003cem\u003erps3*\u003c/em\u003e, \u003cem\u003erps4\u003c/em\u003e, \u003cem\u003erps7\u003c/em\u003e, \u003cem\u003erps10\u003c/em\u003e, \u003cem\u003erps12\u003c/em\u003e, \u003cem\u003erps13\u003c/em\u003e, \u003cem\u003erps14\u003c/em\u003e, \u003cem\u003erps19\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eSuccinate dehydrogenase\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003esdh3\u003c/em\u003e, \u003cem\u003esdh4\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eRibosomal RNAs\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003errn5\u003c/em\u003e, \u003cem\u003errn18\u003c/em\u003e, \u003cem\u003errn26\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003ctr\u003e \u003ctd align=\"left\" colname=\"c1\"\u003e \u003cp\u003eTransfer RNA\u003c/p\u003e \u003c/td\u003e \u003ctd align=\"left\" colname=\"c2\"\u003e \u003cp\u003e\u003cem\u003etrnC-GCA\u003c/em\u003e, \u003cem\u003etrnD-GUC\u003c/em\u003e, \u003cem\u003etrnE-UUC\u003c/em\u003e, \u003cem\u003etrnF-GAA\u003c/em\u003e, \u003cem\u003etrnfM-CAU\u003c/em\u003e, \u003cem\u003etrnG-GCC\u003c/em\u003e, \u003cem\u003etrnH-GUG\u003c/em\u003e, \u003cem\u003etrnI-CAU\u003c/em\u003e, \u003cem\u003etrnK-UUU\u003c/em\u003e, \u003cem\u003etrnL-CAA\u003c/em\u003e, \u003cem\u003etrnM-CAU\u003c/em\u003e, \u003cem\u003etrnN-GUU\u003c/em\u003e, \u003cem\u003etrnP-UGG\u003c/em\u003e, \u003cem\u003etrnQ-UUG\u003c/em\u003e, \u003cem\u003etrnS-GCU\u003c/em\u003e, \u003cem\u003etrnS-GGA\u003c/em\u003e, \u003cem\u003etrnS-UGA\u003c/em\u003e, \u003cem\u003etrnV-GAC\u003c/em\u003e, \u003cem\u003etrnW-CCA\u003c/em\u003e, \u003cem\u003etrnY-GUA\u003c/em\u003e\u003c/p\u003e \u003c/td\u003e \u003c/tr\u003e \u003c/tbody\u003e \u003c/colgroup\u003e \u003c/table\u003e\u003c/div\u003e \u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eNote\u003c/strong\u003e: Gene* indicates that the gene had intron, * indicates the number of introns\u0026nbsp;\u003c/p\u003e\n \u003cdiv id=\"Sec3\" class=\"Section2\"\u003e \u003ch2\u003eRepeat sequence analysis\u003c/h2\u003e \u003cp\u003eSimple sequence repeats (SSRs), known as microsatellite sequences, are tandem repeats, consisting of several nucleotides (usually 1\u0026ndash;6) up to several tens of nucleotides [\u003cspan citationid=\"CR15\" class=\"CitationRef\"\u003e15\u003c/span\u003e]. A total of 318 SSR sequences were identified in the mitogenome of \u003cem\u003eS. maritima\u003c/em\u003e. Mononucleotide A/T repeats were the most prevalent with 199 mononucleotide repeats accounting for 63% of the total SSRs. Additionally, 32 dinucleotide repeats, accounted for 10% of the total SSRs, while trinucleotide and hexanucleotide repeats were less numerous and occurred only in intergenic or intronic regions. There were 16 trinucleotide repeats, 56 tetranucleotide repeats, 56 tetranucleotide repeats, 11 pentanucleotide repeats and 4 hexanucleotide repeats, accounting for 5%, 18%, 3% and 1% of the total SSRs, respectively (Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e2\u003c/span\u003e). Repeats of each base in SSRs (Fig.\u0026nbsp;\u003cspan refid=\"Fig8\" class=\"InternalRef\"\u003e3\u003c/span\u003e) were also counted. A and T repeats were the most frequent, appearing 86 times, followed by C (15 times), G (12 times), and AT (10 times). TA and AT had similar counts (11). Repetitions of the remaining base were all below 5, and there were 69 types of base repeats, and A and T repeated 8 times was frequently detected. There were two types of dispersed repeats in the mitogenome, forward repeats (28) and palindrome repeats (22). Thirty-three long tandem repeats (LTRs), were identified in the mitogenome of \u003cem\u003eSuriana maritima\u003c/em\u003e (Table S1). The size of these tandem repeat units, which ranged from 5 bp to 27 bp in length. The longest duplicate unit was 114 bp (13,865\u0026ndash;13,979), the shortest was only 26 bp (414,564\u0026ndash;414,590).\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec4\" class=\"Section2\"\u003e \u003ch2\u003eCodon usage bias\u003c/h2\u003e \u003cp\u003eThe codon usage statistics for protein-coding genes (PCGs) are shown in Table\u0026nbsp;5. A total of 10,963 codons are used for 39 PCGs in the mitogenome of \u003cem\u003eSuriana maritima\u003c/em\u003e. There exist AT mutation bias in the coding genes given that the base A and T were used in high frequency in the third-codon position compared to other bases (C v.s. G). The most frequent codon was UUU (Phe), which appeared 403 times, followed by AAA (Lys) with 293 times. The least used CGC encoding arginine (Arg) appeared 65 times, followed by GGC encoding glycine (Gly) (79 times). The three stop codons UAA, UGA, and UAG were recorded 158, 181, and 207 times in the whole mitogenome, respectively, demonstrating a preference for UAG.\u003c/p\u003e \u003cp\u003eThe Relative synonymous codon usage (RSCU) is usually used to describe the codon usage preferences of each amino acid. RSCU was visually evaluated using ggplot2 [\u003cspan citationid=\"CR16\" class=\"CitationRef\"\u003e16\u003c/span\u003e] in R, as shown in Table S2 and Fig.\u0026nbsp;\u003cspan refid=\"Fig9\" class=\"InternalRef\"\u003e4\u003c/span\u003e. The codons for methionine (Met), tryptophan (Trp), serine (Ser), and arginine (Arg) showed no preference (RSCU\u0026thinsp;=\u0026thinsp;1). Their codon counterparts are AUG (also the start codon), UGG, UCC, and CGG. There were 29 codons with RSCU\u0026thinsp;\u0026gt;\u0026thinsp;1 (including a termination codon UAG), indicating a preference for these codons (Fig.\u0026nbsp;\u003cspan refid=\"Fig9\" class=\"InternalRef\"\u003e4\u003c/span\u003e and Table S2). For example, arginine had a strong preference for AGA (RSCU\u0026thinsp;=\u0026thinsp;1.49) and glycine for GGA (RSCU\u0026thinsp;=\u0026thinsp;1.44).\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec5\" class=\"Section2\"\u003e \u003ch2\u003eGene transfer between mitochondrial and plastid genomes\u003c/h2\u003e \u003cp\u003eUsing BLAST v2.10.1 to screen fragments of the mitogenome and plastid genomes of \u003cem\u003eSuriana. maritima\u003c/em\u003e showing over 80% identity and performed a homology analysis [\u003cspan citationid=\"CR17\" class=\"CitationRef\"\u003e17\u003c/span\u003e]. we found tremendous genetic residues of plastids in the mitogenome, which means that sequence transfer is quite common between the two organelle genomes. We identified a total of 83 homologous sequences (Table S3), of which 30 were longer than 1000 bp and the longest was 4379 bp. As determined using TBtools [\u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e] (Fig.\u0026nbsp;\u003cspan refid=\"Fig10\" class=\"InternalRef\"\u003e5\u003c/span\u003e), we detected substantial collinearity between fragments on mitochondria and plastids. Using the plastid genome as a reference for annotation and found identified 41 plastid genes in mitochondria (Table S4), including 28 CDS and 13 tRNA, with a total of 30,834 bp of homologous sequences.\u003c/p\u003e \u003cp\u003eThe homologous sequences accounted for 18.8% of the plastid genome and 6.7% of the mitogenome, indicating that the plastid genome of \u003cem\u003eSuriana maritima\u003c/em\u003e is a rich source of foreign sequences in the mitogenome. In particular, 16 plastid genes (\u003cem\u003eycf3\u003c/em\u003e, \u003cem\u003epsaA, psaB\u003c/em\u003e, \u003cem\u003ematK\u003c/em\u003e, \u003cem\u003eatpB\u003c/em\u003e, \u003cem\u003eatpI\u003c/em\u003e, \u003cem\u003erps2\u003c/em\u003e, \u003cem\u003erps4\u003c/em\u003e, \u003cem\u003eatpF\u003c/em\u003e, \u003cem\u003erps7\u003c/em\u003e, \u003cem\u003erpl23\u003c/em\u003e, \u003cem\u003eatpH\u003c/em\u003e, \u003cem\u003epetN\u003c/em\u003e, \u003cem\u003etrnC-GCA\u003c/em\u003e, \u003cem\u003etrnI-CAU\u003c/em\u003e, and \u003cem\u003etrnS\u003c/em\u003e-\u003cem\u003eGGA\u003c/em\u003e) have been completely transferred into the mitogenome (Fig.\u0026nbsp;\u003cspan refid=\"Fig11\" class=\"InternalRef\"\u003e6\u003c/span\u003e).\u003c/p\u003e \u003cp\u003eMapping the 29 genes transferred from the plastids to mitochondria with the transcriptome data, 20 genes can distinguish between mitochondria and plastid genome, the highest expression is in 24 transcripts, and the average expression of normal plastid genes and mitochondrial genes is 100, so it is assumed that the expression of the genes that have been transferred is low (Table S7).\u003c/p\u003e \u003c/div\u003e"},{"header":"Discussion","content":"\u003cp\u003e \u003cb\u003eAssembly of a high-quality mitogenome of\u003c/b\u003e \u003cb\u003eSuriana maritima\u003c/b\u003e\u003c/p\u003e \u003cp\u003eCompared with plastid genome assembly, the assembly of the mitochondrial genome is more difficult. Firstly, there is no effective method to enrich plant mitochondria before DNA extraction [\u003cspan citationid=\"CR19\" class=\"CitationRef\"\u003e19\u003c/span\u003e]. Second, the mitochondrial structure is extremely diverse, and the plant mitogenome shows substantial variation in size, with frequent structural rearrangements, even within closely related species [\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e, \u003cspan citationid=\"CR21\" class=\"CitationRef\"\u003e21\u003c/span\u003e]. For example, in the family Cucurbitaceae, the mitogenome of \u003cem\u003eCitrullus lanatus\u003c/em\u003e is 379 kb [\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e], while that of \u003cem\u003eCucumis sativus\u003c/em\u003e is 2.74 Mb [\u003cspan citationid=\"CR22\" class=\"CitationRef\"\u003e22\u003c/span\u003e], which is seven times the size of the former. Even greater variation has been detected within the genus \u003cem\u003eSilene\u003c/em\u003e, with estimates ranging from 253 kb to 11 Mb [\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e]. Several technical limitations using the data of second genome sequencing may affect the quality of mitogenome assembly as well. Therefore, it is challenging to ascertain whether an assembly is complete or not.\u003c/p\u003e \u003cp\u003eIn this study the mitogenome was assembled from total DNAs with a hybrid assembly strategy, combining the unitig sequences assembled from short Illumina reads and contigs assembled from long Nanopore reads. This strategy can avoid false positives caused by the polishing strategy. During assembly of the \u003cem\u003eS. maritima\u003c/em\u003e mitogenome, the depth at several sites determined by mapping to Illumina reads was relatively low (data not shown). This may be explained by assembly errors or may reflect differences among tissue types, as has been found in other plant species (Fig.\u0026nbsp;\u003cspan refid=\"Fig12\" class=\"InternalRef\"\u003e7\u003c/span\u003e).We thus performed error correction with the second-generation data (Fig.\u0026nbsp;\u003cspan refid=\"Fig13\" class=\"InternalRef\"\u003e8\u003c/span\u003e); for two loci with low depth we used PCR and Sanger sequencing to obtain a high-quality mitogenome. We obtained the first complete mitogenome for \u003cem\u003eS. maritima\u003c/em\u003e in \u003cem\u003eSuriana\u003c/em\u003e (family Surianaceae), which is expected to provide a useful reference for follow-up studies of the function and structure of plant mitochondria. Bioinformatic predictions must be further validated by quantitative PCR experiments, Sanger sequencing, Southern blot, and electronic microscopy [\u003cspan citationid=\"CR24\" class=\"CitationRef\"\u003e24\u003c/span\u003e, \u003cspan citationid=\"CR25\" class=\"CitationRef\"\u003e25\u003c/span\u003e].\u003c/p\u003e \u003cp\u003e \u003cb\u003eStructural characteristics of the\u003c/b\u003e \u003cb\u003eSuriana maritima\u003c/b\u003e \u003cb\u003emitogenome\u003c/b\u003e\u003c/p\u003e \u003cp\u003eThe mitogenome of \u003cem\u003eS. maritima\u003c/em\u003e is a circular structure (Fig.\u0026nbsp;\u003cspan refid=\"Fig6\" class=\"InternalRef\"\u003e1\u003c/span\u003e). The structure of plant mitogenomes shows great instability [\u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e], and various structures have been reported, including linear, branching, and polychromosomal structures. The mitogenome of the garden rocket contains six main ring structures and four small subring molecules, which may be due to the complex structure of the repetitive sequences [\u003cspan citationid=\"CR27\" class=\"CitationRef\"\u003e27\u003c/span\u003e]. A multichromosomal mitogenome structure has been verified in various angiosperms, including \u003cem\u003eCucumis sativus\u003c/em\u003e, \u003cem\u003eSilene gallica\u003c/em\u003e, \u003cem\u003eAmborella trichopoda\u003c/em\u003e, and parasitic plants [\u003cspan citationid=\"CR5\" class=\"CitationRef\"\u003e5\u003c/span\u003e, \u003cspan additionalcitationids=\"CR29\" citationid=\"CR28\" class=\"CitationRef\"\u003e28\u003c/span\u003e\u0026ndash;\u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e]. However, the typical mitogenome structure consists of ring molecules [\u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e], as observed in \u003cem\u003eLeucaena trichandra\u003c/em\u003e [\u003cspan citationid=\"CR32\" class=\"CitationRef\"\u003e32\u003c/span\u003e], and \u003cem\u003eDalbergia odorifera\u003c/em\u003e [\u003cspan citationid=\"CR9\" class=\"CitationRef\"\u003e9\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eRepeat sequence-mediated homologous recombination is universal in plant mitogenomes [\u003cspan citationid=\"CR33\" class=\"CitationRef\"\u003e33\u003c/span\u003e, \u003cspan citationid=\"CR34\" class=\"CitationRef\"\u003e34\u003c/span\u003e]. The large number of repeats (\u0026gt;\u0026thinsp;1000 bp) may lead to a more complex structure, which can also explain why there are fewer genes in the mitogenome than the plastid genome, despite its much larger length. In the assembly of the \u003cem\u003eS. maritima\u003c/em\u003e mitogenome, we also identified repetitive sequences suggesting substantial recombination (Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e2\u003c/span\u003e). Plant mitogenomes are rich in repetitive sequences, accounting for up to 38% of the genome size [\u003cspan citationid=\"CR26\" class=\"CitationRef\"\u003e26\u003c/span\u003e]; however, the origin of repetitive sequences remains unclear. There were 318 simple repeats, 33 long tandem repeats, and 50 dispersed repeats in \u003cem\u003eS. maritima\u003c/em\u003e (Fig.\u0026nbsp;\u003cspan refid=\"Fig7\" class=\"InternalRef\"\u003e2\u003c/span\u003e, Table S1). Based on plant mitogenome sequences available to data, the content and composition of plant mitochondrial repeat sequences differ substantially[\u003cspan citationid=\"CR35\" class=\"CitationRef\"\u003e35\u003c/span\u003e], indicating that these sequences were obtained independently during evolution [\u003cspan citationid=\"CR36\" class=\"CitationRef\"\u003e36\u003c/span\u003e]. Therefore, repeated sequences in the plant mitogenome are closely related to recombination [\u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e], resulting in a highly complex plant mitochondrial structure and causing male abortion in plants.\u003c/p\u003e \u003cp\u003eMitochondrial functional genes are highly conserved [\u003cspan citationid=\"CR37\" class=\"CitationRef\"\u003e37\u003c/span\u003e], and the majority of genomic variation is found in intergenic regions [\u003cspan citationid=\"CR38\" class=\"CitationRef\"\u003e38\u003c/span\u003e]. Intergenic sequences are characterized by a large number of repeated sequences and imported sequences [\u003cspan citationid=\"CR30\" class=\"CitationRef\"\u003e30\u003c/span\u003e] as well as intron length variation and pseudogene factors [\u003cspan citationid=\"CR39\" class=\"CitationRef\"\u003e39\u003c/span\u003e]. Repetitive sequences appear in highly variable intergenic regions [\u003cspan citationid=\"CR31\" class=\"CitationRef\"\u003e31\u003c/span\u003e], frequent structural rearrangements [\u003cspan citationid=\"CR40\" class=\"CitationRef\"\u003e40\u003c/span\u003e], substantial gene loss, and the transfer of endogenous and exogenous DNA [\u003cspan citationid=\"CR41\" class=\"CitationRef\"\u003e41\u003c/span\u003e], The long repeats in the mitogenome also had a high frequency of recombination. Short repeats had a low recombination frequency, consistent with previous results [\u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e42\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eIn addition, mitochondrial PCGs have strong codon preference. UUU encoding phenylalanine (Phe) is the most frequently used codon, while the CGC encoding arginine (Arg) is the least codon in the PCGs in the mitogenomes of \u003cem\u003eS. maritima\u003c/em\u003e.\u003c/p\u003e \u003cdiv id=\"Sec7\" class=\"Section2\"\u003e \u003ch2\u003e\u003cb\u003eGene transfer between mitochondria and plastid genomes\u003c/b\u003e\u003c/h2\u003e \u003cp\u003eGenes transferred from the plastid genome are commonly found in plant mitogenomes, typically representing 1\u0026ndash;12% of the total length [\u003cspan citationid=\"CR43\" class=\"CitationRef\"\u003e43\u003c/span\u003e]. In contrast, the transfer of sequences from the plant mitogenome into plastid genomes is nearly impossible, since the plastid genome is relatively conserved and does not accept the integration of foreign DNA fragments [\u003cspan citationid=\"CR44\" class=\"CitationRef\"\u003e44\u003c/span\u003e]. The transfer of plastid DNA to the mitogenome occurred at least 300\u0026nbsp;million years ago [\u003cspan citationid=\"CR45\" class=\"CitationRef\"\u003e45\u003c/span\u003e]. No insertions of plastid and nuclear genes were found in the mitogenome of bryophytes, indicating that the absorption of foreign DNA by plant mitochondria occurred during the evolution of vascular plants [\u003cspan citationid=\"CR46\" class=\"CitationRef\"\u003e46\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eCompared with previous studies of other taxa, the mitogenome of \u003cem\u003eS. maritima\u003c/em\u003e had the highest rates of transfer from the plastid genome. Homologous sequences with a total length of 30,834 bp accounted for 18.8% of the plastid genome and 6.7% of the mitogenome of \u003cem\u003eS. maritima\u003c/em\u003e (Table S3). The smaller mitogenome of \u003cem\u003eCitrullus lanatus\u003c/em\u003e contains about 23 kb of transferred plastid sequences. More 5% of the mitogenomes of \u003cem\u003eCucurbita pepo\u003c/em\u003e is derived from plastid sequences of (approximately 113 kb) [\u003cspan citationid=\"CR47\" class=\"CitationRef\"\u003e47\u003c/span\u003e]. Plastid-to-mitochondrion sequences are 1.67 kb in \u003cem\u003eSilene\u003c/em\u003e and 3.52 kb in \u003cem\u003eVigna radiata\u003c/em\u003e [\u003cspan citationid=\"CR7\" class=\"CitationRef\"\u003e7\u003c/span\u003e]. In \u003cem\u003eBupleurum chinense\u003c/em\u003e, the total length of sequences transferred from the plastid genome to the mitogenome was found to be 11,144 bp, accounting for 2.56% of the mitogenome [\u003cspan citationid=\"CR8\" class=\"CitationRef\"\u003e8\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eEarly studies have shown that plastid-derived tRNA genes are required for the translation of plant mitogenomes [\u003cspan citationid=\"CR23\" class=\"CitationRef\"\u003e23\u003c/span\u003e]. The plastid fragments that were transferred to mitochondria mostly include genes, pseudogenes, and intergenomic sequences [\u003cspan citationid=\"CR3\" class=\"CitationRef\"\u003e3\u003c/span\u003e]. Most functional genes are tRNA genes, while other genes are generally not expressed and many become pseudogenes gradually over time [\u003cspan citationid=\"CR48\" class=\"CitationRef\"\u003e48\u003c/span\u003e, \u003cspan citationid=\"CR49\" class=\"CitationRef\"\u003e49\u003c/span\u003e]. Here, we identified 16 full-length genes that have been completely transferred from the plastid of \u003cem\u003eS. maritima\u003c/em\u003e to the mitogenome (i.e., \u003cem\u003eycf3\u003c/em\u003e, \u003cem\u003epsaA, psaB\u003c/em\u003e, \u003cem\u003ematK\u003c/em\u003e, \u003cem\u003eatpB\u003c/em\u003e, \u003cem\u003eatpI\u003c/em\u003e, \u003cem\u003erps2\u003c/em\u003e, \u003cem\u003erps4\u003c/em\u003e, \u003cem\u003eatpF\u003c/em\u003e, \u003cem\u003erps7\u003c/em\u003e, \u003cem\u003erpl23\u003c/em\u003e, \u003cem\u003eatpH\u003c/em\u003e, \u003cem\u003epetN\u003c/em\u003e, \u003cem\u003etrnC-GCA\u003c/em\u003e, \u003cem\u003etrnI-CAU\u003c/em\u003e, and \u003cem\u003etrnS\u003c/em\u003e-\u003cem\u003eGGA\u003c/em\u003e) (Fig.\u0026nbsp;\u003cspan refid=\"Fig11\" class=\"InternalRef\"\u003e6\u003c/span\u003e). However, these genes might not function in mitochondria, and they might undergo pseudogenization [\u003cspan citationid=\"CR50\" class=\"CitationRef\"\u003e50\u003c/span\u003e]. Pseudogenes mainly encode important proteins; however, complete plastid protein genes have also been found in \u003cem\u003eVitis vinifera\u003c/em\u003e [\u003cspan citationid=\"CR51\" class=\"CitationRef\"\u003e51\u003c/span\u003e]. For example, the \u003cem\u003erpl32\u003c/em\u003e gene from the plastid has been transferred into in the subfamily Thalictroideae (family Ranunculaceae)[\u003cspan citationid=\"CR52\" class=\"CitationRef\"\u003e52\u003c/span\u003e]. Three complete genes in the mitogenomes migrated from the plastid genome of okra, including \u003cem\u003epsaA\u003c/em\u003e, \u003cem\u003erps7\u003c/em\u003e, and \u003cem\u003epsbJ\u003c/em\u003e, in addition to several plastid-derived gene fragments [\u003cspan citationid=\"CR53\" class=\"CitationRef\"\u003e53\u003c/span\u003e].\u003c/p\u003e \u003cp\u003eIn addition, we found that \u003cem\u003eS. maritima\u003c/em\u003e has substantial differences in fragment position caused by the insertion of plastid genes into the mitogenome. Intracellular gene transfer may be responsible for the high degree of rearrangement [\u003cspan citationid=\"CR54\" class=\"CitationRef\"\u003e54\u003c/span\u003e]. Since the plastid genome fragments are well-aligned with the original plastid genome sequence, this gene transfer may cause the disassembly of the mitogenome. The mitochondrial and nuclear genomes can transfer DNA sequences in both directions. However, most studies have found that plastid genome fragments are only transferred to the nuclear and mitogenomes, while other genomes are not transferred to the plastid, and the plastid genome tends not to integrate foreign DNA [\u003cspan citationid=\"CR55\" class=\"CitationRef\"\u003e55\u003c/span\u003e, \u003cspan citationid=\"CR56\" class=\"CitationRef\"\u003e56\u003c/span\u003e].\u003c/p\u003e \u003c/div\u003e"},{"header":"Conclusions","content":"\u003cp\u003eIn this study, we successfully assembled the mitogenome of \u003cem\u003eS. maritima\u003c/em\u003e with a high quality by using both Nanopore and Illumina reads, enabling a comprehensive comparison of the organelle genomes of \u003cem\u003eS. maritima\u003c/em\u003e. A single circular master molecule represents the mitogenome of \u003cem\u003eS. maritima\u003c/em\u003e. The chloroplast genome of \u003cem\u003eS. maritima\u003c/em\u003e provided abundant foreign sequences in the mitogenome, including 41 plastid genes among 83 mitochondrial plastid DNA sequences with a total length of 30,834 bp. The transferred sequences accounted for 18.8% of the plastid genome and 6.7% of the mitogenome, which is much higher than previous estimates in Fabales. This study provided strong evidence for gene transfer between the mitochondria and plastids genes. Additional sampling from all families in the order are needed to more fully understand their complex history and the functional interplay between plastid and mitochondrial genetics.\u003c/p\u003e"},{"header":"Materials and methods","content":"\u003cdiv id=\"Sec10\" class=\"Section2\"\u003e \u003ch2\u003eTaxon sampling, DNA extraction and sequencing\u003c/h2\u003e \u003cp\u003eWe collected \u003cem\u003eS. maritima\u003c/em\u003e in Xisha Islands (China) and cultivated plants at the South China Botanical Garden, CAS. Total genomic DNA was extracted from fresh leaves using a modified cetyltrimethylammonium bromide (CTAB) method [\u003cspan citationid=\"CR57\" class=\"CitationRef\"\u003e57\u003c/span\u003e]. Second-generation sequencing was conducted using the Illumina HiSeq-2500 platform with a read length of 150 bp. Sequencing produced a total of 5.6 Gb of raw data. For Oxford Nanopore sequencing, purified DNA was prepared for long-read sequencing following the protocol provided with the SQK-LSK109 genomic sequencing kit (Oxford Nanopore Technologies, Oxford, UK). Extraction, database constuction, and sequencing were completed by Beijing Baimaike Biotechnology Co., Ltd.]\\\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec11\" class=\"Section2\"\u003e \u003ch2\u003eMitogenome assembly\u003c/h2\u003e \u003cp\u003eWe initially assembled the mitogenome of \u003cem\u003eS. maritima\u003c/em\u003e using Illumina short reads. GetOrganelle v1.7.7.0 was used for assembly with the parameter setting \u0026ldquo;embplant_mt\u0026rdquo; and a custom mitochondrial database as references [\u003cspan citationid=\"CR58\" class=\"CitationRef\"\u003e58\u003c/span\u003e]. The output contained 238 contigs of 276\u0026ndash;89,145 bp in length, with a total length of 637,303 bp. When visualizing the raw GFA file produced by GetOrganelle in Bandage v0.8.1 [\u003cspan citationid=\"CR59\" class=\"CitationRef\"\u003e59\u003c/span\u003e], the mitogenome consisted of a network of connected contigs (Figure S1). Unnecessary contigs were manually deleted. After many rounds of verification, a complete closed-loop structure was obtained.\u003c/p\u003e \u003cp\u003eThe published mitochondrial CDS sequences of \u003cem\u003eLeucaena trichandra\u003c/em\u003e and \u003cem\u003eVicia faba\u003c/em\u003e were used as references (among which \u003cem\u003eLeucaena trichandra\u003c/em\u003e contained 56 CDS sequences and \u003cem\u003eVicia faba\u003c/em\u003e contained 61 CDS sequences). Minimap2 [\u003cspan citationid=\"CR60\" class=\"CitationRef\"\u003e60\u003c/span\u003e] was used to identify putative mitochondrial Nanopore reads of \u003cem\u003eS. maritima\u003c/em\u003e. Then, Canu [\u003cspan citationid=\"CR61\" class=\"CitationRef\"\u003e61\u003c/span\u003e] to perform self-correction and trimming of the identified putative mitochondrial Nanopore reads. The parameters are set to: genomeSize\u0026thinsp;=\u0026thinsp;2m, corThreads\u0026thinsp;=\u0026thinsp;64; For the assembly result, LoRDEC [\u003cspan citationid=\"CR62\" class=\"CitationRef\"\u003e62\u003c/span\u003e] was used to correct the reads twice and trim once, with the following parameter settings: -k\u0026thinsp;=\u0026thinsp;19, -s\u0026thinsp;=\u0026thinsp;3; The parameters for retrimming and assembly were genomeSize\u0026thinsp;=\u0026thinsp;2m, minReadLength\u0026thinsp;=\u0026thinsp;5000, and correctedErrorRate\u0026thinsp;=\u0026thinsp;0.134 to obtain 11 contigs with lengths of 26,663\u0026ndash;514,650 bp (Table S5).\u003c/p\u003e \u003cp\u003eThe Canu assembly result showed that contig1 was\"suggestCircular.\" Considering that the length of this contig was the longest among the 11 contigs, it might represent the true mitogenome sequence of \u003cem\u003eS. maritima\u003c/em\u003e. To further verify whether contig1 is a complete mitogenome, Illumina reads (5.6 Gb) were mapped to the 41 genes (24 core genes and 17 variable genes) of angiosperm mitogenomes using Bowtie2 [\u003cspan citationid=\"CR63\" class=\"CitationRef\"\u003e63\u003c/span\u003e], and the mapped reads were extracted using Samtools v1.9 [\u003cspan citationid=\"CR64\" class=\"CitationRef\"\u003e64\u003c/span\u003e] with the parameter -bF 4, generating a much smaller subset of Illumina mitochondrial reads. We then calculated their depth of coverage using Samtools. It was found that 39 genes had a depth of coverage of \u0026gt;\u0026thinsp;5000\u0026times;, except \u003cem\u003erps2\u003c/em\u003e and \u003cem\u003erps11\u003c/em\u003e (2\u0026ndash;16 for \u003cem\u003erps2\u003c/em\u003e and \u003cem\u003erps11\u003c/em\u003e) (Table S6). These 39 genes except \u003cem\u003erps2\u003c/em\u003e and \u003cem\u003erps11\u003c/em\u003e exist in the mitogenome of \u003cem\u003eS. maritima\u003c/em\u003e. The above 39 genes were used as a reference genome to annotate contig1, revealing that contig1 contained 39 genes except for \u003cem\u003erps2\u003c/em\u003e and \u003cem\u003erps11\u003c/em\u003e. Therefore, contig1 may contain the complete information of the mitogenome of \u003cem\u003eS. maritima\u003c/em\u003e. Then, Pilon [\u003cspan citationid=\"CR65\" class=\"CitationRef\"\u003e65\u003c/span\u003e] was used for gap filling and sequence correction with default settings until its depth reached 5000\u0026ndash;8000, and this was used in subsequent analyses.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec12\" class=\"Section2\"\u003e \u003ch2\u003eGenome annotation\u003c/h2\u003e \u003cp\u003eThe web-based tool Public MITOFY Analysis was used to identify genes [\u003cspan citationid=\"CR20\" class=\"CitationRef\"\u003e20\u003c/span\u003e]. We also revised the start and stop codons of genes based on similar genes, manually checked by MITOFY against other sequenced mitogenomes. Mitogenome annotation was performed using the BLASTN alignment tools of the National Center for Biotechnology Information (NCBI) database (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://www.ncbi.nlm.nih.gov/\u003c/span\u003e\u003cspan address=\"https://www.ncbi.nlm.nih.gov/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e) with the gene bank of angiosperm mitogenomes as reference sequences. The tRNAs were annotated using tRNAscan-SE [\u003cspan citationid=\"CR66\" class=\"CitationRef\"\u003e66\u003c/span\u003e] with default settings. The circular mitogenome map was drawn using OGDRAW [\u003cspan citationid=\"CR67\" class=\"CitationRef\"\u003e67\u003c/span\u003e]. The final mitogenome of \u003cem\u003eS. maritima\u003c/em\u003e has been deposited in GenBank (Accession number: OQ933798).\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec13\" class=\"Section2\"\u003e \u003ch2\u003eAnalysis of mitogenome characteristics\u003c/h2\u003e \u003cp\u003eThe GC content was determined using the cusp program provided by EMBOSS [\u003cspan citationid=\"CR68\" class=\"CitationRef\"\u003e68\u003c/span\u003e]. The SSRs of the mitogenome of \u003cem\u003eS. maritima\u003c/em\u003e were analyzed using Misa [\u003cspan citationid=\"CR69\" class=\"CitationRef\"\u003e69\u003c/span\u003e] (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://webblast.ipk-gatersleben.de/misa/\u003c/span\u003e\u003cspan address=\"https://webblast.ipk-gatersleben.de/misa/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e), with a size of one to six nucleotides, thresholds of eight, five, four, three, three, and three, separately, and a minimum distance between two SSRs of 100 bp. REPuter [\u003cspan citationid=\"CR70\" class=\"CitationRef\"\u003e70\u003c/span\u003e, \u003cspan citationid=\"CR71\" class=\"CitationRef\"\u003e71\u003c/span\u003e] (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://bibiserv.cebitec.uni-bielefeld.de/reputer/\u003c/span\u003e\u003cspan address=\"https://bibiserv.cebitec.uni-bielefeld.de/reputer/\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e) was used to calculate palindromic repeats, forward repeats, reverse repeats, and complement repeats with the following settings: hamming distance of three and minimal repeat size of 30 bp. LTR identification was performed using the \"Advanced\" module of Tandem Repeats Finder [\u003cspan citationid=\"CR72\" class=\"CitationRef\"\u003e72\u003c/span\u003e] (\u003cspan class=\"ExternalRef\"\u003e\u003cspan class=\"RefSource\"\u003ehttps://tandem.bu.edu/trf/trf.html\u003c/span\u003e\u003cspan address=\"https://tandem.bu.edu/trf/trf.html\" targettype=\"URL\" class=\"RefTarget\"\u003e\u003c/span\u003e\u003c/span\u003e) with default settings. Codon preference (synonymous codon usage, RSCU) of mitochondrial PCGs of the \u003cem\u003eS. maritima\u003c/em\u003e mitogenome was calculated using CodonW.\u003c/p\u003e \u003c/div\u003e \u003cdiv id=\"Sec14\" class=\"Section2\"\u003e \u003ch2\u003eIdentification of plastid gene transfer to the mitogenome\u003c/h2\u003e \u003cp\u003eThe complete plastids genome of \u003cem\u003eS. maritima\u003c/em\u003e (NC_047313.1) [\u003cspan citationid=\"CR73\" class=\"CitationRef\"\u003e73\u003c/span\u003e, \u003cspan citationid=\"CR74\" class=\"CitationRef\"\u003e74\u003c/span\u003e] was downloaded from the NCBI Organelle Genome Resources database. Plastid gene transfer to the mitogenome were identified using BLAST [\u003cspan citationid=\"CR75\" class=\"CitationRef\"\u003e75\u003c/span\u003e], with the following parameter settings:- evalue 1e-5, -word_size 9, -gapopen 5, -gapextend 2, -reward 2, -penalty-3, and -dust no [\u003cspan citationid=\"CR42\" class=\"CitationRef\"\u003e42\u003c/span\u003e]. Screening criteria were set with an identity threshold of \u0026ge;\u0026thinsp;80%. The identification results were visualized with reference to collinearity analysis uusing the \"Advanced Circos\" module of TBtools [\u003cspan citationid=\"CR18\" class=\"CitationRef\"\u003e18\u003c/span\u003e].\u003c/p\u003e \u003c/div\u003e"},{"header":"Abbreviations","content":"\u003cdiv class=\"DefinitionList\"\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003ePCG\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eProtein-coding genes\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003etRNA\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eTransfer RNA\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003erRNA\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eRibosomal RNA\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eMitogenome\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eMitochondrial genome\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eNCBI\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eNational Center for Biotechnology Information\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eSSR\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eSimple sequence repeat\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eBLAST\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eBasic Local Alignment Search Tool\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eLTR\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eLong tandem repeats\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003cdiv class=\"DefinitionListEntry\"\u003e \u003cdiv class=\"Term\"\u003eRSCU\u003c/div\u003e \u003cdiv class=\"Description\"\u003e \u003cp\u003eRelative Synonymous Codon Usage CDS:Coding sequence.\u003c/p\u003e \u003c/div\u003e \u003c/div\u003e \u003c/div\u003e"},{"header":"Declarations","content":"\u003cp\u003e\u003cstrong\u003eEthics approval and consent to participate\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe material involved in the article does not involve ethical conflicts. Field studies complied with local legislation, and appropriate permissions were granted before the samples were collected from the South China Botanical Garden.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConsent for publication\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eNot applicable.\u0026nbsp;\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eCompeting interests\u0026nbsp;\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe authors declare that they have no competing interests.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAvailability of data and materials\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThe complete mitogenome sequence of \u003cem\u003eSuriana. maritima\u003c/em\u003e has been deposited in the GenBank database under the accession number OQ933798 (these numbers were automatically generated by NCBI and refer to the same sample). The associated BioProject, SRA, and Bio-Sample numbers are PRJxxxxx, SRRxxxx, and SAMNxxxxx, respectively.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eFunding\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThis work was financially supported by\u0026nbsp;the National Natural Science Foundation of China (32070222, 32170232), the National Key Research and Development Program of China (2021YFC3100405) and the Guangdong Provincial Special Fund for Natural Resource Affairs on Ecology and Forestry Construction (GDZZDC20228704).\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eAuthors\u0026apos; contributions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eIn this research, Jian-Xin Li conceived and designed the study. She has completed the data analysis and the first draft of the paper. Runxian Yu helped assemble and annotate the mitogemome, Meng hua Zhang, Miao-Miao Shi, Zhongtao Zhao, Shijin Li, Xiang-Ping Wang, Dianxiang Zhang, Ying Meng, Ze-Long Nie and Tie-Yao Tu have been responsible for supervising the experimental design, data analysis, and the writing and revision of the manuscript. All authors approved the final version and agreed to be accountable for all aspects of the work.\u003c/p\u003e"},{"header":"References","content":"\u003col\u003e\n\u003cli\u003eGualberto, J.M. and K.J. Newton, Plant mitochondrial genomes: dynamics and mechanisms of mutation. Annual Review of Plant Biology, 2017. 68: p. 225-252.\u003c/li\u003e\n\u003cli\u003eBendich, A.J., Reaching for the ring : the study of mitochondrial genome structure. 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Systematic Biology, 2020.\u003c/li\u003e\n\u003cli\u003eJohnson, M., et al., NCBI BLAST: a better web interface. Nucleic Acids Res, 2008. 36(Web Server issue): p. W5-9.\u003c/li\u003e\n\u003c/ol\u003e"}],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":true,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"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":"Gene transfer, Fabales, mitochondrial genome, Suriana maritima, Surianaceae","lastPublishedDoi":"10.21203/rs.3.rs-3948491/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-3948491/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003ch2\u003eBackground\u003c/h2\u003e \u003cp\u003eGene transfer between the plastid and mitochondrial genomes has been reported in several lineages of the legume family (Leguminosae or Fabaceae). However, it is not clear whether these events happened in other families of the order Fabales. We herein generated a high-quality mitochondrial genome of \u003cem\u003eSuriana maritima\u003c/em\u003e in the family Surianaceae, which is closely related to Leguminosae and distributed mainly in extreme environments of tropical coral islands, to understand the gene transfers between orgenelle genomes of \u003cem\u003eS. maritima\u003c/em\u003e and the structural and functional evolution of mitogenomes in Fabales.\u003c/p\u003e\u003ch2\u003eResults\u003c/h2\u003e \u003cp\u003eWe combined Illumina and Nanopore technologies to assemble the mitogenome of \u003cem\u003eS. maritima\u003c/em\u003e. The mitogenome was 458,738 bp in length and contained 39 protein-coding, three ribosomal RNA, and 20 transfer RNA genes. A number of sequences derived from the chloroplast genome of \u003cem\u003eS. maritima\u003c/em\u003e were detected in the mitogenome, including 41 plastid genes among 83 mitochondrial plastid DNA sequences with a total length of 30,834 bp. Transferred genes accounted for 18.8% of the plastid genome and 6.7% of the mitogenome, and these estimates were much higher than those in previous studies of Fabales.\u003c/p\u003e\u003ch2\u003eConclusions\u003c/h2\u003e \u003cp\u003eIn addition to providing a high-quality mitogenome of an additional species in Fabales and the first species in Surianaceae, \u003cem\u003eS. maritima\u003c/em\u003e, our findings advance our understanding of gene transfer between organelle genomes.\u003c/p\u003e","manuscriptTitle":"A high-quality mitochondrial genome of Suriana maritima reveals tremendous gene transfers between the plastid and mitochondrial genomes","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2024-02-20 16:04:34","doi":"10.21203/rs.3.rs-3948491/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":"8b7dd913-b54e-4d25-90bf-1fda49d8b1a2","owner":[],"postedDate":"February 20th, 2024","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2024-06-17T12:51:22+00:00","versionOfRecord":[],"versionCreatedAt":"2024-02-20 16:04:34","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-3948491","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-3948491","identity":"rs-3948491","version":["v1"]},"buildId":"7rjqhiLT3MXkJMwkYKINL","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}