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Article

The Complete Mitochondrial Genome of Ophioglossum vulgatum L. Is with Highly Repetitive Sequences: Intergenomic Fragment Transfer and Phylogenetic Analysis

by
Jing Hao
1,
Yingyi Liang
1,
Yingjuan Su
2,3,* and
Ting Wang
1,*
1
College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
2
School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
3
Research Institute of Sun Yat-sen University in Shenzhen, Shenzhen 518057, China
*
Authors to whom correspondence should be addressed.
Genes 2022, 13(7), 1287; https://doi.org/10.3390/genes13071287
Submission received: 21 June 2022 / Revised: 13 July 2022 / Accepted: 19 July 2022 / Published: 21 July 2022
(This article belongs to the Special Issue Advances in Evolution of Plant Organelle Genome)
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Abstract

:
Many plant mitochondrial (mt) genomes have been sequenced but few in ferns. Ophioglossum vulgatum represents a typical species of fern genus Ophioglossum with medicinal and scientific value. However, its mt genome structure remains to be characterized. This study assembled and annotated the complete O. vulgatum mt genome and presented its structural characters and repeat sequences firstly. Its mt and chloroplast (cp) transfer sequences were explored, and the phylogenetic significance of both mt and cp genomes was also evaluated at the family level. Our results showed that the complete mt genome of O. vulgatum is a single circular genome of 369,673 bp in length, containing 5000 dispersed repetitive sequences. Phylogenetic trees reconstructed from cp and mt genomes displayed similar topologies, but also showed subtle differences at certain nodes. There exist 4818 bp common gene fragments between cp and mt genomes, of which more than 70% are located in tRNA intergenic regions (in mt). In conclusion, we assembled the complete mt genome of O. vulgatum, identified its remarkable structural characters, and provided new insights on ferns. The complementary results derived from mt and cp phylogeny highlighted that some higher taxonomic-level phylogenetic relationships among ferns remain to be resolved.

Graphical Abstract

1. Introduction

The mitochondrion is a semi-autonomous organelle with a genetic system independent of the cell nucleus [1,2]. The mitochondrion plays an important role in metabolic processes. It provides energy for eukaryotes and is the site of ATP synthesis [3]. The mitochondrial (mt) genomes of plants are large and complex, with a length of 200–2000 kbp and a variable structure [4]. The mt genome structure is often described as circles, but its real structure appear diversely as circular, linear, and complex branched [5] (e.g., Cucumis sativus has three circular chromosomes that replicate completely or largely autonomously [6]; and Lactuca sativa has a variety of linear, circular and branched mt genome structures [7]). The complex and variable mt genome structures in plants may be caused by large numbers of repetitive sequences [8]. The sequences enable the mediation of inter- and intramolecular homologous recombination within the mt genome, leading to structure diversity [9]. It is known that the level of repetitive sequence-mediated recombination is also varied [10], with rates associated with repeat sizes [8].
In addition, nuclear and chloroplast (cp) DNA transfers into mt DNA in plants are more frequent in comparison with other eukaryotes [11,12,13,14]. Generally, transfers of mt sequences into cp genome occur much less frequently [15,16]. Typical events of intergenomic fragment transfers detected in higher plants include transfers of mt coxII gene into nucleus via RNA mediation [11] and cp photosynthesis-related genes or fragments into nuclear or mt genomes (Orobanchaceae) [14,17], cp sequences into nucleus (mitochondria as a bridge, Actinidia) [18], and mt sequences into nucleus (Dalbergia odorifera) [3]. These findings suggest that intergenomic fragment transfers may reflect a common evolutionary phenomenon [14], underlining their importance for understanding plant mt genome evolution.
With the advancement of high-throughput sequencing technology, considerable organelle genome data have been applied to phylogenetic research. In particular, the whole cp and mt genome sequences have been noted to be useful barcodes [19,20]. Evolutionary rates of cp genome tend to be slightly faster than those of mt genome [21]. Additionally, cpDNA markers have been more widely used than mtDNA in plant molecular phylogenetic studies. Partially, this is due to the instability of mtDNA size, structure, and sequence content [22]. Nevertheless, the mtDNA encoded genes can be conserved [23] and have the potential to be used in addressing unsolved phylogenetic issues.
Among land plants, Marchantia polymorpha is the first whose mt genome was sequenced [24]. To date (as of June 2022), there are a total of 465 complete plant mt genomes that have been deposited in the National Center for Biotechnology Information (NCBI) Organelle Genome Database. Of those, however, only three are ferns. Mt genome sequence data of ferns are critical for fully understanding mt genome characters of plants, as ferns represent the sister group of seed plants. Family Ophioglossaceae is one of the most fascinating lineages among ferns. It is among the second earliest-diverging lineages of ferns and has the largest known number of nuclear chromosomes [25]. Ophioglossum vulgatum is a typical species of the genus Ophioglossum with significant medicinal and scientific value [26]. The plant is difficult to characterize at the nuclear genome level due to its large number of nuclear chromosomes (2n = 240–1140) [27]. In a previous study, we sequenced the complete cp genome of O. vulgatum [28], but its mt genome remains to be explored.
In this study, in order to reveal the structural features, intergenomic fragment transfers, and phylogenetic usefulness of O. vulgatum mt genome, we conducted the following investigations: (1) the complete mt genome sequence of O. vulgatum was sequenced, assembled, and annotated; (2) the structural characters and repetitive sequences of O. vulgatum mt genome were presented, and the phylogenetic significance of mt simple sequence repeats (SSRs) was evaluated at family level; (3) the consistency and differences in family-level phylogeny reconstructed using mt and cp gene sequences were revealed; and (4) the length, position, and potential function of the genomic fragments transferred between mt and cp genomes were characterized.

2. Materials and Methods

2.1. DNA Extraction, Illumina DNA Library Construction and Sequencing

The plant materials were collected from South China Agricultural University (113°20′ E, 23°9′ N), and fresh leaves of O. vulgatum were selected for total DNA extraction. The total DNA was extracted using a plant DNA extraction kit according to the instructions (CWBIO CW0553, Nanjing, Jiangsu, China). After extraction, the qualified samples were used to construct a paired-end sequencing Illumina DNA library with an insert size of 350 bp. Then, the qPCR and Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) were used for quality control. Sequencing was performed on the Illumina NovaSeq6000 (Illumina, San Diego, CA, USA) high-throughput sequencing platform, and the sequencing strategy was PE150 (Pair-End 150).

2.2. Assembly and Annotation of the mt Genome

High-quality clean reads were obtained after filtering raw reads generated from Illumina high-throughput sequencing. Then, we used the pair-end clean reads and our PacBio Isoform Sequencing (Iso-Seq) full-length transcriptome data to assemble and annotate the mt genome (our full-length transcriptome data was sequenced with PacBio Sequel II platform (Pacific Biosciences, Menlo Park, CA, USA); our RNA Iso-seq sequences and mRNA sequences were deposited in the NCBI Sequence Read Archive (SRA) under the study accession number PRJNA856114). The mtDNA sequence was assembled by using SPAdes v. 3.13.0 with the plasmid method and multi k-mer parameters [29]. The full-length transcripts of O. vulgatum and the mt genome of Polypodiopsida were used as references. Pair-end sequencing reads were then re-aligned to the assembled mt sequences to confirm the assembly and close gaps. The mRNA sequences were mapped to the mt genome with minimap2 and blastn to annotate the mt genes and identify mt RNA editing sites [30,31,32]. The tRNAscan-SE v. 2.0 software was used to predict tRNAs [33]. OGDRAW v. 1.3.1 was used to draw mt genome maps [34]. The complete mt genome was deposited in Genbank under the accession number OL800577.

2.3. Analysis of mt Genome Characters

We selected mt genomes of three bryophytes, three ferns, four gymnosperms, four monocotyledonous angiosperms, and four dicotyledonous angiosperms from NCBI (O. vulgatum mt genome was sequenced in this study) for conducting statistical analysis of mt-encoding protein genes (Table 1). DnaSP v. 6.12.03 was used to calculate nucleotide variability (Pi) values [35]. Mutation sites were mapped to the O. vulgatum mt genome to identify their locations.

2.4. Phylogenetic and Fragment Transfer Analysis of mt and cp Genomes

Mt and cp complete genomes of sampling species (Table 1) were downloaded from Genbank. PhyloSuite (v. 1.2.2, Zhang et al., Wuhan, China) were used to extract the common mt and cp CDS sequences [36]. The MAFFT (v. 7) plugin (based on codons) in PhyloSuite was used for multiple sequence alignment [37]. Then, concatenated data sets of cp and mt common genes were constructed separately. The Gblocks (v. 0.91b) plugin in PhyloSuite was used to optimize protein sequence alignments [38]. A maximum likelihood (ML) phylogenetic tree was constructed using the IQtree (v. 1.6.8) plugin in PhyloSuite (Ultrafast bootstrap, bootstrap = 1000, three bryophytes set as outgroups) [39,40]. For mtDNA, we chose GTR + F + G4 (“GTR” means general time reversible model with unequal rates and unequal base freq, “+F” means empirical base frequencies, and “+G4” means discrete γ model with the number of categories as G4) as the best-fit model based on Bayesian information criterion (BIC). For cpDNA, we selected GTR + F + R3 (“+ R3” means FreeRate model that generalizes the + G model by relaxing the assumption of γ-distributed rates with the number of categories R3) as the best-fit model. In addition, the MrBayes v. 3.2.6 plugin in PhyloSuite was used to conduct the Bayesian inference (BI) [41]. The web tool ITOL v. 5 was used to beautify phylogenetic trees [42]. Homologous sequences between cp and mt genomes were searched by Blast in TBtools (e-value = 1 × 10−5, Num of Hits = 50,000, and Num of Aligns= 25,000) [43]. The Circos plot was drawn using TBtools.

2.5. Identification and Analysis of Repetitive Sequences

SSRs were identified using MISA-web (version 2.1) [44]. Ten, six, five, five, five, and five repeat units were set as the minimum thresholds for the identification of mono-, di-, tri-, tetra-, penta-, and hexa-motif microsatellites, respectively. The maximum length between two SSRs in the composite SSR was set as 0 bp. The web tool REPuter program was used to search the dispersed repeats (Hamming distance = 3; maximum computed repeats = 5000; minimal repeat size = 30; forward (F), reverse (R), complement (C), and palindromic (P) repeats were all permitted) [45,46]. An advanced Circos plot was drawn with TBtools. Finally, we evaluated the phylogenetic significance of SSRs by examining mtSSR characteristics in the context of mt ML tree.

3. Results

3.1. Characters of the Complete mt Genome of O. vulgatum

We successfully assembled the complete mt genome of O. vulgatum. It is a single circular genome with a length of 369,673 bp and a total GC content of 52.14% (Figure 1). We annotated 64 genes including 37 protein coding genes, 24 tRNA genes, and three rRNA genes (Table 2). The longest gene is rrn26 (3283 bp), located in the positive strand; and the shortest are tRNA-Gly (71 bp) and tRNA-Cys (71 bp), located in the positive and negative strands, respectively. Among the 37 protein coding genes, two (rpl2, rps3) contain one intron, two (nad4, nad7) have three introns, and three (nad1, nad2, nad5) contain four introns. RNA editing occurred in 26 genes, accounting for 70.27% of all protein-coding genes. Besides O. vulgatum, we selected three bryophytes, two ferns, four gymnosperms, and four monocotyledonous and four dicotyledonous angiosperms to perform analysis of mt protein coding genes (Table 2 and Table S1). Four ccm (cytochrome c maturation) genes (ccmB, ccmC, ccmFC, and ccmFN) were lost from O. vulgatum in comparison with most selected plants. The ribosomal protein 6 gene (rpl6) was present in three ferns (including O. vulgatum) compared with other selected seed plants. The results were consistent with the analysis of its related species O. californicum [10]. We speculated that the entire cytochrome c pathway may be lost in O. vulgatum.

3.2. Comparative mt Genomic Analysis between O. vulgatum and O. californicum

We compared the mt genomes of O. californicum and O. vulgatum (Figure 2). There were six hypervariable regions between the two species. The maximum Pi value was 0.018, which was derived from the intergenic region between tRNA-Gln (TTG) and tRNA-Leu (TAA) in O. vulgatum. The minimum Pi value was 0.002, which was from the intergenic region between nad5 and nad9. The remaining four variable loci were located as follows: the intergenic region between tRNA- Asp (GTC) and tRNA-Ser (GCT), the intergenic region between tRNA-Ser (GCT) and tRNA-Arg (TCG), the intergenic region between nad4 and rps11, and the intron 3 of nad7. Our results revealed that there were six hypervariable regions between the two species, which were mainly located in mt intergenic regions.

3.3. Comparative Phylogenetic Analysis Based on mt and cp Genomic Sequences

We concatenated all common coding genes from mt and cp genomes and used the matrices to infer phylogenetic trees based on mt and cp data, respectively. ML trees are shown in Figure 3, and BI trees are shown in Figure S1 (as ML and BI trees have similar topologies, we focused on the ML tree here). Phylogenetic trees reconstructed from cp and mt data have roughly the same topology for the major branches. Bryophytes, ferns, gymnosperms, and angiosperms were clustered in four branches in both cp and mt trees. Branch lengths in the cp tree tended to be longer than those in the mt tree (except for C. nucifera). Two Ophioglossum species formed a monophyletic clade in both mt and cp trees, and P. nudum diverged earlier. In the mt tree, bryophytes formed a topology as ((P. patens, A. punctatus), M. polymorpha). By contrast, in the cp tree, A. punctatus was the sister to a clade containing P. patens and M. polymorpha. For gymnosperms, the cp tree showed that C. taitungensis and G. biloba clustered together. However, the mt tree showed that the two species did not. Both mt and cp trees showed that L. tulipifera and the other four monocots were clustered together, but with weak support (bootstrap = 64/74). The remaining dicots formed a clade. Their branching pattern in the cp tree was ((N. nucifera, A. thaliana), A. kusnezoffii); but in the mt tree, it was (N. nucifera, (A. thaliana, A. kusnezoffii)), which was consistent with the APG IV system [47]. The phylogenetic results indicated that the phylogenetic trees reconstructed from cp and mt genome sequences had roughly the same topologies, but there existed subtle differences in the branching structure. The complementary information provided by mt and cp trees highlighted that some significant phylogenetic relationships remain to be clarified.

3.4. Intergenomic Fragment Transfers between mt and cp Genomes

We identified 14 common gene fragments between the cp and mt genomes of O. vulgatum (Figure 4 and Table S2). The fragment lengths ranged from 52 to 683 bp, with a total length of 4818 bp. In the cp genome, the common gene fragments were symmetrically distributed in IRa (Inverted repeat a) and IRb regions, located in rrn16S, rrn23S, tRNA-Ala (TGC), and the tRNA-Ala (TGC)–rrn23S intergenic region. In the mt genome, the common gene fragments were located in rrn18, nad5–nad9 intergenic region, and tRNA-Asp (GTC)–tRNA-Phe (GAA) intergenic region. We speculated that there existed fragment transfers between mitochondrion and chloroplast genomes of O. vulgatum.

3.5. Analysis of Repetitive Sequences

A total of 5000 dispersed repetitive sequences were detected in the O. vulgatum mt genome. Their lengths ranged from 108 to 7435 bp. The sequences contained 2408 palindromic (P) repeats and 2592 forward (F) repeats. There were seven repeats larger than 1000 bp. Positions of the repeats are shown in Figure 5 and Table S3. In addition, a total of 20 SSRs were detected in the O. vulgatum mt genome, with sizes ranging from 10 to 48 bp (Figure 5 and Table S4). The SSR types were as follows: seven mononucleotides (mono-), with G/C as repeating unit; seven dinucleotides (di-), with TC/CT (5), AC (1), and GA (1) as repeating units; two trinucleotides (tri-), with GTG/TTA as repeating unit; one tetranucleotide (tetra-) with AAAG as repeating unit; one pentanucleotide (penta-), with AAGTA as repeating unit; and two hexanucleotides (hexa-), with TCCAAC as repeating unit. Most SSRs were located in intergenic regions, except for four SSRs that were in the introns of nad4, nad5, and nad7.
Previously, we noted that distribution characteristics of cp SSRs may provide useful phylogenic information at the genus level [48]. Here, we further evaluated the phylogenetic significance of mt SSRs based on the mt tree (Figure 6). No association was found between the distribution characteristics of mt SSRs and phylogenetic relationships at family level. Nevertheless, O. vulgatum and O. californium showed consistent mtSSR distribution patterns. W. mirabilis has no mono- repeating units. L. tulipifera is a dicot, and its mtSSR distribution showed similarity with two Arecaceae monocots. Noteworthily, L. tulipifera and the two Arecaceae monocots were clustered in the same clade in the mt tree.

4. Discussion

It has been well noted that a considerable number of mt genes have been lost or functionally transferred during mt evolution [11,49]. In this study, O. vulgatum was found to be lacking four mt ccm genes (ccmB, ccmC, ccmFC, and ccmFN) in comparison with most other sampling plants. To consolidate the mt gene loss, we also mapped the four ccm gene sequences to our full-length transcriptome datasets. No corresponding transcripts were detected. Proteins encoded by the mt ccm genes function in the maturation pathway of cytochrome c and are important electron transporters in the mt respiratory chain of plants [50]. Moreover, the ccm genes were also detected as lost in the bryophyte A. punctatus but not in P. patens and other examined plants. We speculated the functions of the mt ccm genes might have been replaced by nuclear counterparts [49]. On the other hand, a rpl6 gene addition was observed in the mt genomes of three ferns (P. nudum, O. vulgatum, and O. californicum). It cannot be excluded that the rpl6 gene may have been present in the ancestor of vascular plants and functionally transferred to the nucleus or lost in certain lineages during evolution [10,11,49].
There exist frequent gene transfers from cp to mt genomes in plants [15]. For example, photosynthesis-related genes have been observed to be transferred from cp to mt genomes in Orobanchaceae [14,17]. Here, we identified 14 common gene fragments between the cp and mt genomes in O. vulgatum, with a total length of 4818 bp (as shown in mt genome, Table S2). The results underscore extensive gene or fragment transfers between the two O. vulgatum genomes, but we were unable to determine the transfer direction. Previous studies indicate that the mt genome tends to takes up cp sequences rather than the opposite [15,16]. Thus, we hypothesize that the common fragments detected in O. vulgatum could be generated by cp to mt transfers. Importantly, Miyata et al. (1998) detected some plastid-derived sequences in the rice mt genome encoding tRNA genes [51]. Here, we also noticed that more than 70% of the transferred fragments were located in tRNA intergenic regions in the O. vulgatum mt genome. In addition, Notsu et al. (2002) showed that cp fragments may be first integrated into mt genome and then transferred to the nucleus (i.e., the mt genome functions as an intermediate) [52].
This study revealed considerable repetitive sequences in the mt genome of O. vulgatum like in other plants [53]. A total of 5000 dispersed repetitive sequences were detected with lengths ranging from 108 to 7435 bp. Repetitive sequences may mediate frequent recombination, facilitating genome diversity [9]. However, Guo et al. (2017) noted that the mt genomes of ferns O. californicum and P. nudum maintain an extremely low level of active recombination, although their mt genomes are highly repetitive [10]. This highlights the possibility that the frequency of repetitive sequence-mediated mt recombination may vary greatly across plant lineages. Additionally, we also identified a total of 20 mtSSRs in O. vulgatum with sizes ranging from 10 to 48 bp. Previously, the distribution characteristics of cp SSRs were found to be capable of providing phylogenetic signals at the genus level [48]. In this study, similar characteristics were indeed observed in the mtSSRs of O. vulgatum and O. californium. However, no association was found between the mtSSR characteristics and phylogenetic relationships at the family level. It is noteworthy that mtSSRs of the dicot L. tulipifera show similar characteristics with monocots, and in the mt ML tree, L. tulipifera is found to cluster with monocots. These results indicate that the phylogenetic significance of the mtSSR patterns deserves to be further explored in the future.
The complete cp genome sequences have been extensively used to reconstruct plant phylogeny [3,21]. In contrast, mt genome sequences appear to have been relatively scarce in this respect [21]. Nevertheless, mt and cp sequences may provide complementary information for phylogenetic inference [54,55]. Here, we performed a comparative phylogenetic analysis by using the datasets constructed from the shared cp or mt genes. Similar family-level phylogenetic relationships have been reconstructed, but there are subtle differences: the phylogenetic position of C. taitungensis and G. biloba in the gymnosperms, and the position of N. nucifera and L. tulipifera in angiosperms. These inconsistencies suggest that some higher taxonomic-level phylogenetic controversies remain to be solved. They also restate the importance of facilitating plant mitochondrial phylogenomic studies.

5. Conclusions

Based on this study, our conclusions are as follows: (1) the complete mt genome of O. vulgatum is a single circular genome with extensive repetitive sequences; its mt encoded ccm genes are lost, and the mt genome has six intergenic regions that are hypervariable; (2) distribution characteristics of mt SSRs may not provide phylogenetic signals at the family level; (3) phylogenetic trees reconstructed from cp and mt genome sequences show roughly the same topologies, but there are subtle differences; and (4) a total of 4818 bp common gene fragments have been identified between the O. vulgatum cp and mt genomes. This study provides new mt genome resources on ferns and highlights the importance of reexamining plant phylogenetic relationships based on both cp and mt genome sequences.

Supplementary Materials

The following supporting information can be downloaded at: https://www.mdpi.com/article/10.3390/genes13071287/s1, Figure S1: The phylogenic Bayesian inference trees of mt (left) and cp (right) based on common gene datasets of selected species. The numbers beside the branches represent the posterior probability. The different color boxes represent different plant groups (Bryophytes, ferns, gymnosperms, monocots, and dicots); Table S1: Statistical information on mitochondrial genes of 18 species; Table S2: Location information on the common fragments between mitochondrial and chloroplast genomes; Table S3: Locations of the dispersed repetitive sequences in the mitochondrial genome of O. vulgatum; Table S4: SSR sequences and location information (IGS, intergenic spacer; p1, p2, p3, p4, p5, and p6 represent mono-, di-, tri-, tetra-, penta-, and hexa-SSRs, respectively).

Author Contributions

T.W. and Y.S. conceived and designed the research. J.H. and Y.L. contributed to the sample preparation, genome sequencing, and analysis of the data. J.H. wrote the original draft. T.W. and Y.S. revised the manuscript. All authors have read and agreed to the published version of the manuscript.

Funding

This work was supported by the National Natural Science Foundation of China (31872670 and 32071781), Guangdong Basic and Applied Basic Research Foundation (2021A1515010911), Science and Technology Projects in Guangzhou (202206010107), and Project of Department of Science and Technology of Shenzhen City, Guangdong, China (JCYJ20190813172001780 and JCYJ20210324141000001).

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

The complete mt genome was deposited in Genbank of NCBI under the accession number OL800577. The data supporting the findings of this study are available from the corresponding author upon reasonable request.

Acknowledgments

We would like to thank J.C. in the Science Corporation of Gene (Guangzhou, China) for his help in the sequencing process.

Conflicts of Interest

The authors declare no conflict of interest.

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Figure 1. Mitochondrial genome map of O. vulgatum. The total length of the mitochondrial genome is 369,673 bp. Genes shown on the inside of the circle are transcribed clockwise, whereas those on the outside are transcribed counter-clockwise. Genes containing introns are marked by an asterisk (*).
Figure 1. Mitochondrial genome map of O. vulgatum. The total length of the mitochondrial genome is 369,673 bp. Genes shown on the inside of the circle are transcribed clockwise, whereas those on the outside are transcribed counter-clockwise. Genes containing introns are marked by an asterisk (*).
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Figure 2. Hypervariable regions between O. vulgatum and O. californicum. The horizontal axis shows the location information for O. vulgatum mitochondrial genome, and the vertical axis shows the Pi values.
Figure 2. Hypervariable regions between O. vulgatum and O. californicum. The horizontal axis shows the location information for O. vulgatum mitochondrial genome, and the vertical axis shows the Pi values.
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Figure 3. Maximum likelihood (ML) trees reconstructed by using concatenated datasets of common mitochondrial (left) and chloroplast (right) genes of representative species. Red numbers below the branches are bootstrap values. Values above the branches are branch lengths. The boxes with different colors represent different plant groups (the bryophytes, ferns, gymnosperms, monocots, and dicots).
Figure 3. Maximum likelihood (ML) trees reconstructed by using concatenated datasets of common mitochondrial (left) and chloroplast (right) genes of representative species. Red numbers below the branches are bootstrap values. Values above the branches are branch lengths. The boxes with different colors represent different plant groups (the bryophytes, ferns, gymnosperms, monocots, and dicots).
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Figure 4. Locations of the transferred fragments between mitochondrial and chloroplast genomes. Green circle represents mitochondrial genome, and orange circle chloroplast genome. Blue and red lines inside the circle correspond to fragment lengths more or less than 100 bp, respectively. Ends of the same line indicate the location of common gene fragments.
Figure 4. Locations of the transferred fragments between mitochondrial and chloroplast genomes. Green circle represents mitochondrial genome, and orange circle chloroplast genome. Blue and red lines inside the circle correspond to fragment lengths more or less than 100 bp, respectively. Ends of the same line indicate the location of common gene fragments.
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Figure 5. Simple sequence repeats (SSRs) and dispersed repetitive sequences in the mitochondrial genome of O. vulgatum. Black lines on the blue circle indicate the SSR locations. Lines inside the circle show the distribution of dispersed repetitive sequences; green lines represent forward (F) repeats, and orange lines represent palindromic (P) repeats (light green and orange lines correspond to lengths less than 200 bp).
Figure 5. Simple sequence repeats (SSRs) and dispersed repetitive sequences in the mitochondrial genome of O. vulgatum. Black lines on the blue circle indicate the SSR locations. Lines inside the circle show the distribution of dispersed repetitive sequences; green lines represent forward (F) repeats, and orange lines represent palindromic (P) repeats (light green and orange lines correspond to lengths less than 200 bp).
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Figure 6. Simple sequence repeats (SSRs) characteristic of 18 representative species and their association with phylogeny. P1, p2, p3, p4, p5, p6, and c (*) represent mono-, di-, tri-, tetra-, penta-, hexa-, and compound SSRs, respectively. Clades in the tree are highlighted with color boxes. Horizontal axis in the right figure presents the number of different SSR types.
Figure 6. Simple sequence repeats (SSRs) characteristic of 18 representative species and their association with phylogeny. P1, p2, p3, p4, p5, p6, and c (*) represent mono-, di-, tri-, tetra-, penta-, hexa-, and compound SSRs, respectively. Clades in the tree are highlighted with color boxes. Horizontal axis in the right figure presents the number of different SSR types.
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Table
Table 1. Information on sampling species.
Table 1. Information on sampling species.
NamesFamilyGroupGenbank Accessions (mt)Genbank Accessions (cp)
Marchantia paleaceaMarchantiaceaeBryophyteNC_001660NC_001319
Physcomitrium patensFunariaceae BryophyteNC_007945KY126308
Anthoceros punctatusAnthocerotaceae BryophyteNC_049003MN544310
Ophioglossum californicumOphioglossaceaeFernKX171637NC_020147
O. vulgatumOphioglossaceaeFernOL800577MZ066610
Psilotum nudumPsilotaceaeFernKX171638,
KX171639 		NC_003386
Welwitschia mirabilisWelwitschiaceaeGymnospermNC_029130NC_010654
Pinus taedaPinaceaeGymnospermNC_039746NC_021440
Cycas taitungensisCycadaceae GymnospermNC_010303NC_009618
Ginkgo bilobaGinkgoaceae GymnospermNC_027976NC_016986
Oryza sativa Indica GroupPoaceaeAngiosperm
(monocot)		NC_007886NC_008155
Triticum aestivumPoaceaeAngiosperm
(monocot)		GU985444NC_002762
Phoenix dactyliferaArecaceaeAngiosperm
(monocot)		NC_016740NC_013991
Cocos nuciferaArecaceaeAngiosperm
(monocot)		NC_031696NC_022417
Liriodendron tulipiferaMagnoliaceae Angiosperm
(dicot)		NC_021152NC_008326
Aconitum kusnezoffiiRanunculaceaeAngiosperm
(dicot)		NC_053920KT820671
Nelumbo nuciferaNelumbonaceaeAngiosperm
(dicot)		NC_030753NC_025339
Arabidopsis thalianaBrassicaceaeAngiosperm
(dicot)		Y08501NC_000932
Table
Table 2. Mitochondrial protein-coding genes of O. vulgatum.
Table 2. Mitochondrial protein-coding genes of O. vulgatum.
Gene TypeGene Name
ATPase subunitsatp1, atp4, atp6, atp8, atp9
Apocytochrome bcob
Cytochrome c oxidase subunitscox1, cox2, cox3
Ribosomal proteinsrpl2, rpl5, rpl6, rpl16, rps1, rps2, rps3, rps4, rps7, rps10, rps11, rps12, rps13, rps14, rps19
MaturasematR
Sec-independent protein translocase protein mttB
NADH dehydrogenase subunitsnad1, nad2, nad3, nad4, nad4L, nad5, nad6, nad7, nad9
Succinate dehydrogenase cytochrome subunitssdh3, sdh4
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Hao, J.; Liang, Y.; Su, Y.; Wang, T. The Complete Mitochondrial Genome of Ophioglossum vulgatum L. Is with Highly Repetitive Sequences: Intergenomic Fragment Transfer and Phylogenetic Analysis. Genes 2022, 13, 1287. https://doi.org/10.3390/genes13071287

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Hao J, Liang Y, Su Y, Wang T. The Complete Mitochondrial Genome of Ophioglossum vulgatum L. Is with Highly Repetitive Sequences: Intergenomic Fragment Transfer and Phylogenetic Analysis. Genes. 2022; 13(7):1287. https://doi.org/10.3390/genes13071287

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Hao, Jing, Yingyi Liang, Yingjuan Su, and Ting Wang. 2022. "The Complete Mitochondrial Genome of Ophioglossum vulgatum L. Is with Highly Repetitive Sequences: Intergenomic Fragment Transfer and Phylogenetic Analysis" Genes 13, no. 7: 1287. https://doi.org/10.3390/genes13071287

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