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(A) Chloroplast genome of Aeginetia indica. (B) Mitochondrial genome of A. indica. Top and bottom genes are transcribed in forward and reverse directions, respectively. (A) Chloroplast genome of Aeginetia indica. (B) Mitochondrial genome of A. indica. Top and bottom genes are transcribed in forward and reverse directions, respectively.
Source publication
Orobanchaceae have become a model group for studies on the evolution of parasitic flowering plants, and Aeginetia indica, a holoparasitic plant, is a member of this family. In this study, we assembled the complete chloroplast and mitochondrial genomes of A. indica. The chloroplast and mitochondrial genomes were 56,381 bp and 401,628 bp long, respec...
Contexts in source publication
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... previous study [31] showed that the plastid genome of A. indica is 86,212 bp in length with an LSC (Large single Copy), SSC (Small Single Copy), and two IRs. However, we found the complete plastid genome of A. indica (GenBank accession number: MW851293) is 56,381 bp in length and contains an LSC, SSC, and only one IR ( Figure 1) together with 26 protein coding genes. ...
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... coverage of A. indica in the present study was 6089X ( Figure S1). In contrast, the coverage of the plastid in the previous study of A. indica had gaps and low coverage values ( Figures S1 and S2). ...
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... coverage of A. indica in the present study was 6089X ( Figure S1). In contrast, the coverage of the plastid in the previous study of A. indica had gaps and low coverage values ( Figures S1 and S2). Furthermore, the GC content of the plastid genome in this study (32.9%) was higher than in the previous study (34.4%), and 18 tRNAs was smaller in the present study. ...
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... assembled A. indica mitogenome was 491,631 bp long (GenBank accession number: MW851294) with a GC content of 43.5% (Figure 1). The average coverage of the A. indica mitogenome was 1379.9X ( Figure S4). ...
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... repeats ranged in length from 37 to 419 bp with a total length of 8384 bp. We identified 12 chloroplast genome fragments in the mitochondrial genome that included genes and intergenic regions (Figures 1 and 2, Table S2). The fragments ranged from 57 to 154 bp. ...
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... the A. indica mitochondrial genome had a smaller plastid-derived sequence size than other Lamiales (Figure 2). A total of 34 complete native mitochondria protein coding genes and one complete chloroplast protein coding gene (atpI) were annotated in the mitogenome with 15 tRNAs (11 native mitochondrial tRNAs and four plastid-derived tRNAs) and three rRNAs (Figure 1, Tables S3-S5). The A. indica mitochondrial genome did not contain ribosomal protein subunit genes (rps1, rps2, rps7, rps11, and rps19), and two respiratory genes (shd3, and sdh4), which have been lost in angiosperms (Table S3) [14,23,33,34]. ...
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... assembled A. indica mitogenome was 491,631 bp long (GenBank accession number: MW851294) with a GC content of 43.5% (Figure 1). The average coverage of the A. indica mitogenome was 1379.9X ( Figure S4). ...
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... repeats ranged in length from 37 to 419 bp with a total length of 8384 bp. We identified 12 chloroplast genome fragments in the mitochondrial genome that included genes and intergenic regions (Figures 1 and 2, Table S2). The fragments ranged from 57 to 154 bp. ...
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... the A. indica mitochondrial genome had a smaller plastid-derived sequence size than other Lamiales (Figure 2). A total of 34 complete native mitochondria protein coding genes and one complete chloroplast protein coding gene (atpI) were annotated in the mitogenome with 15 tRNAs (11 native mitochondrial tRNAs and four plastid-derived tRNAs) and three rRNAs (Figure 1, Tables S3-S5). The A. indica mitochondrial genome did not contain ribosomal protein subunit genes (rps1, rps2, rps7, rps11, and rps19), and two respiratory genes (shd3, and sdh4), which have been lost in angiosperms (Table S3) [14,23,33,34]. ...
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... domains in candidate ORFs were predicted using TMHMM v2.0 [58]. Figure S1: Comparison of Aeginetia indicla plastid genome length and coverage between this study (A) and previous study (B). Figure S2: Comparison of the plastid genome sequences of this study and previous study generated using mVISTA program. Figure S3: Phylogenetic tree of 34 species (Table S1) taxa based on 14 chloroplast genes in the cp genome. ...
Citations
... Horizontal gene transfer (HGT) is a process that transmits genetic material between species or individuals without mating. Plant mitochondria are especially susceptible to HGT as numerous foreign mitochondrial genes have been uncovered in various seed plants [1][2][3][4][5][6][7][8][9][10][11][12]. In contrast, only a few cases of integrated mitochondrial DNA were reported in plastids [13][14][15][16][17][18]. ...
Background
Horizontal gene transfer (HGT) events have rarely been reported in gymnosperms. Gnetum is a gymnosperm genus comprising 25‒35 species sympatric with angiosperms in West African, South American, and Southeast Asian rainforests. Only a single acquisition of an angiosperm mitochondrial intron has been documented to date in Asian Gnetum mitogenomes. We wanted to develop a more comprehensive understanding of frequency and fragment length distribution of such events as well as their evolutionary history in this genus.
Results
We sequenced and assembled mitogenomes from five Asian Gnetum species. These genomes vary remarkably in size and foreign DNA content. We identified 15 mitochondrion-derived and five plastid-derived (MTPT) foreign genes. Our phylogenetic analyses strongly indicate that these foreign genes were transferred from diverse eudicots—mostly from the Rubiaceae genus Coptosapelta and ten genera of Malpighiales. This indicates that Asian Gnetum has experienced multiple independent HGT events. Patterns of sequence evolution strongly suggest DNA-mediated transfer between mitochondria as the primary mechanism giving rise to these HGT events. Most Asian Gnetum species are lianas and often entwined with sympatric angiosperms. We therefore propose that close apposition of Gnetum and angiosperm stems presents opportunities for interspecific cell-to-cell contact through friction and wounding, leading to HGT.
Conclusions
Our study reveals that multiple HGT events have resulted in massive amounts of angiosperm mitochondrial DNA integrated into Asian Gnetum mitogenomes. Gnetum and its neighboring angiosperms are often entwined with each other, possibly accounting for frequent HGT between these two phylogenetically remote lineages.
... Previously, HGT events in parasitic plants have been widely discussed. For example, some chloroplast genes in the mitogenome of the Aphyllon epigalium were transferred from its host's chloroplast genome [70]; the plastid-origin rpl32 gene was reported to be transferred to the nuclear genome in the subfamily Thalictroideae [71]; the atpI gene found in the mitogenome of Aeginetia indica is believed to have originated from the chloroplast genome of another angiosperm [72]; In the genus Geranium, we observed multiple instances of horizontal gene transfers involving ribosomal proteins. However, studies suggest that these transferred genes from the plastid might be nonfunctional in the mitochondria, potentially becoming pseudogenes during mitogenome evolution [72]. ...
... For example, some chloroplast genes in the mitogenome of the Aphyllon epigalium were transferred from its host's chloroplast genome [70]; the plastid-origin rpl32 gene was reported to be transferred to the nuclear genome in the subfamily Thalictroideae [71]; the atpI gene found in the mitogenome of Aeginetia indica is believed to have originated from the chloroplast genome of another angiosperm [72]; In the genus Geranium, we observed multiple instances of horizontal gene transfers involving ribosomal proteins. However, studies suggest that these transferred genes from the plastid might be nonfunctional in the mitochondria, potentially becoming pseudogenes during mitogenome evolution [72]. Because we lack the nuclear genome data for B. schreberi, this study only analyzes the sequence transfer between the two organellar genomes of B. schreberi. ...
Brasenia schreberi, a plant species traditionally utilized in Chinese medicine and cuisine, represents an early evolutionary stage among flowering plants (angiosperms). While the plastid genome of this species has been published, its mitochondrial genome (mitogenome) has not been extensively explored, with a notable absence of thorough comparative analyses of its organellar genomes. In our study, we had assembled the entire mitogenome of B. schreberi utilizing the sequencing data derived from both Illumina platform and Oxford Nanopore. The B. schreberi mitogenome mostly exists as six circular DNA molecules, with the largest being 628,257 base pairs (bp) and the smallest 110,220 bp, amounting to 1.49 megabases (Mb). Then we annotated the mitogenome of B. schreberi. The mitogenome encompasses a total of 71 genes: 40 of these are coding proteins genes (PCGs), 28 are genes for transfer RNA (tRNA), and the remaining 3 are genes for ribosomal RNA (rRNA). In the analysis of codon usage, we noted a unique codon preference specific to each amino acid. The most commonly used codons exhibited an average RSCU of 1.36, indicating a noticeable bias in codon selection. In the repeat sequence analysis, a total of 553 simple sequence repeats (SSRs) were identified, 1,822 dispersed repeats (comprising 1,015 forward and 807 palindromic repeats), and 608 long terminal repeats (LTRs). Additionally, in the analysis of homologous sequences between organelle genomes, we detected 38 homologous sequences derived from the plastid genome, each exceeding 500 bp, within the B. schreberi mitochondrial genome. Notably, ten tRNA genes (trnC-GCA, trnM-CAU, trnI-CAU, trnQ-UUG, trnN-GUU, trnT-GGU, trnW-CCA, trnA-UGC, trnI-GAU, and trnV-GAC) appear to have been completely transferred from the chloroplast to the mitogenome. Utilizing the Deepred-mt to predict the RNA editing sites in the mitogenome, we have identified 675 high-quality RNA editing sites in the 40 mitochondrial PCGs. In the final stage of our study, we performed an analysis of colinearity and inferred the phylogenetic relationship of B. schreberi with other angiosperms, utilizing the mitochondrial PCGs as a basis. The results showed that the non-coding regions of the B. schreberi mitogenome are characterized by an abundance of repetitive sequences and exogenous sequences, and B. schreberi is more closely related with Euryale ferox.
... Annotation of these homologous sequences unveiled incomplete fragments originating from the cpDNA. Previous research indicates that, such homologous fragments vary among species in length and sequence [41]. Furthermore, genes migrating from chloroplasts to mitochondria often become pseudogenes over time, lacking functional significance, possibly due to sequence recombination [26,42]. ...
Background
Primulina hunanensis, a troglobitic plant within the Primulina genus of Gesneriaceae family, exhibits robust resilience to arid conditions and holds great horticultural potential as an ornamental plant. The work of chloroplast genome (cpDNA) has been recently accomplished, however, the mitochondrial genome (mtDNA) that is crucial for plant evolution has not been reported.
Results
In this study, we sequenced and assembled the P. hunanensis complete mtDNA, and elucidated its evolutionary and phylogenetic relationships. The assembled mtDNA spans 575,242 bp with 43.54% GC content, encompassing 60 genes, including 37 protein-coding genes (PCGs), 20 tRNA genes, and 3 rRNA genes. Notably, high number of repetitive sequences in the mtDNA and substantial sequence translocation from chloroplasts to mitochondria were observed. To determine the evolutionary and taxonomic positioning of P. hunanensis, a phylogenetic tree was constructed using mitochondrial PCGs from P. hunanensis and 32 other taxa. Furthermore, an exploration of PCGs relative synonymous codon usage, identification of RNA editing events, and an investigation of collinearity with closely related species were conducted.
Conclusions
This study reports the initial assembly and annotation of P. hunanensis mtDNA, contributing to the limited mtDNA repository for Gesneriaceae plants and advancing our understanding of their evolution for improved utilization and conservation.
... Complete cemA loss is reported in many lineages (Wicke et al., 2011), among which are Hydnoraceae, the holoparasitic members of perianth-bearing Piperales (Jost et al., 2022). Currently, there is no evidence for intracellular gene transfer of cemA to the mitochondrial genome in Piperales (Yu et al., 2023), unlike in holoparasitic Aeginetia (Choi and Park, 2021). Until further evidence arises, we consider the disrupted cemA copies in Piperales as pseudogenes. ...
Premise
Many plastomes of autotrophic Piperales have been reported to date, describing a variety of differences. Most studies focused only on a few species or a single genus, and extensive, comparative analyses have not been done. Here, we reviewed publicly available plastome reconstructions for autotrophic Piperales, reanalyzed publicly available raw data, and provided new sequence data for all previously missing genera. Comparative plastome genomics of >100 autotrophic Piperales were performed.
Methods
We performed de novo assemblies to reconstruct the plastomes of newly generated sequence data. We used Sanger sequencing and read mapping to verify the assemblies and to bridge assembly gaps. Furthermore, we reconstructed the phylogenetic relationships as a foundation for comparative plastome genomics.
Results
We identified a plethora of assembly and annotation issues in published plastome data, which, if unattended, will lead to an artificial increase of diversity. We were able to detect patterns of missing and incorrect feature annotation and determined that the inverted repeat (IR) boundaries were the major source for erroneous assembly. Accounting for the aforementioned issues, we discovered relatively stable junctions of the IRs and the small single‐copy region (SSC), whereas the majority of plastome variations among Piperales stems from fluctuations of the boundaries of the IR and the large single‐copy (LSC) region.
Conclusions
This study of all available plastomes of autotrophic Piperales, expanded by new data for previously missing genera, highlights the IR‐LSC junctions as a potential marker for discrimination of various taxonomic levels. Our data indicates a pseudogene‐like status for cemA and ycf15 in various Piperales. Based on a review of published data, we conclude that incorrect IR‐SSC boundary identification is the major source for erroneous plastome assembly. We propose a gold standard for assembly and annotation of high‐quality plastomes based on de novo assembly methods and appropriate references for gene annotation.
... This occurrence is especially prevalent in higher plants, where they have incorporated several plastid sequences from neighboring chloroplasts. This evolutionary process has transpired over an extended timeframe and is likely ongoing (Choi and Park, 2021;Garcia et al., 2021;Lin et al., 2022). Currently, the availability of mitogenome resources for the plants is limited. ...
Aglaia odorata, native to Guangdong, Guangxi, and Hainan provinces in China, has long been utilized as an herbal remedy in ancient China. In this study, we assembled and annotated the complete mitochondrial genome (mitogenome) of A. odorata, which spans a total length of 537,321 bp. Conformation of the A. odorata recombination was verified through PCR experiments and Sanger sequencing. We identified and annotated 35 protein-coding genes (PCGs), 22 tRNA genes, and 3 rRNA genes within the mitogenome. Analysis of repeated elements revealed the presence of 192 SSRs, 29 pairs of tandem repeats, and 333 pairs of dispersed repeats in the A. odorata mitogenome. Additionally, we analyzed codon usage and mitochondrial plastid DNAs (MTPTs). Twelve MTPTs between the plastome and mitogenome of A. odorata were identified, with a combined length of 2,501 bp, accounting for 0.47% of the mitogenome. Furthermore, 359 high-confidence C to U RNA editing sites were predicted on PCGs, and four selected RNA editing sites were specially examined to verify the creation of start and/or stop codons. Extensive genomic rearrangement was observed between A. odorata and related mitogenomes. Phylogenetic analysis based on mitochondrial PCGs were conducted to elucidate the evolutionary relationships between A. odorata and other angiosperms.
... Here, we identi ed 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]. ...
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.
... Eight complete CDSs (rps7, rpl23, ndhB, psbJ, psbL, psbF, psbE, and petG) were found to migrate from the plastome to the mitogenome in R. chingii and to some other plastid gene fragments. Remarkably, seven genes (rps7, rpl23, ndhB, psbE, psbF, psbJ, and psbL) were simultaneously annotated in both the mitogenome and plastome; however, other genes transferred from the plastid might have undergone pseudogenization in the mitogenome [77,78]. In angiosperms, it is common for tRNA genes to transfer from the plastome to the mitogenome [79]. ...
Rehmannia chingii is an important medicinal plant with immense value in scientific research. However, its mitochondrial genome (mitogenome) has not yet been characterized. Herein, based on whole-genome Illumina short reads and PacBio HiFi reads, we obtained the complete mitogenome of R. chingii through a de novo assembly strategy. We carried out comparative genomic analyses and found that, in comparison with the plastid genome (plastome) showing a high degree of structural conservation, the R. chingii mitogenome structure is relatively complex, showing an intricate ring structure with 16 connections, owing to five repetitive sequences. The R. chingii mitogenome was 783,161 bp with a GC content of 44.8% and contained 77 genes, comprising 47 protein-coding genes (CDS), 27 tRNA genes, and 3 rRNA genes. We counted 579 RNA editing events in 47 CDS and 12,828 codons in all CDSs of the R. chingii mitogenome. Furthermore, 24 unique sequence transfer fragments were found between the mitogenome and plastome, comprising 8 mitogenome CDS genes and 16 plastome CDS genes, corresponding to 2.39% of the R. chingii mitogenome. Mitogenomes had shorter but more collinear regions, evidenced by a comparison of the organelles of non-parasitic R. chingii, hemiparasitic Pedicularis chinensis, and holoparasitic Aeginetia indica in the Orobanchaceae family. Moreover, from non-parasitic to holoparasitic species, the genome size in the mitogenomes of Orobanchaceae species did not decrease gradually. Instead, the smallest mitogenome was found in the hemiparasitic species P. chinensis, with a size of 225,612 bp. The findings fill the gap in the mitogenome research of the medicinal plant R. chingii, promote the progress of the organelle genome research of the Orobanchaceae family, and provide clues for molecular breeding.
... Notably, Rubisco large subunit, cytochrome b6/f complex subunits, and NADH dehydrogenase subunit are typically considered photosynthesis-related genes (Dobrogojski, et al. 2020), and fragments of their transfer are identified in the mitogenomes. However, as previously reported, these genes transferred from the plastid to mitogenome might not be functional, and could undergo pseudogenization as the mitochondrial genome evolves (Choi and Park 2021). ...
Saccharum belongs to the Andropogoneae and cultivars species in Saccharum contributes nearly 80% sugar production of the world. To explore the genomic studies in Saccharum, we assembled 15 complete mitochondrial genomes (mitogenome) of three foundation species (Saccharum spontaneum, S. robustum and S. officinarum) using Illumina and Oxford Nanopore Technologies sequencing data. The mitogenomes of the three species were divided into a total of eight types based on contig numbers and linkages. All mitogenomes in the three species encoded 51 unique genes including 32 protein-coding, 3 ribosomal RNA (rRNA) and 16 transfer RNA (tRNA) genes. The existence of long and short repeat-mediated recombinations in the mitogenome of S. officinarum and S. robustum was revealed and confirmed through PCR validation. Furthermore, employing comparative genomics and phylogenetic analyses of the organelle genomes, we unveiled the evolutionary relationships and history of the major interspecific lineages in the Saccharum genus. Phylogenetic analyses of homologous fragments between S. officinarum and S. robustum showed that S. officinarum and S. robustum are phylogenetically distinct, and that they were likely parallel rather than domesticated. The variations between ancient (S. sinense and S. barberi) and modern cultivated species (S. hybrid) possibly resulted from hybridization involving different S. officinarum accessions. Lastly, this project reported the first graph-based mitogenome of three Saccharum species, and systematic comparison of the structural organization, evolutionary processes, and pan-structural variation of the Saccharum mitochondrial genomes revealed the differential features of the Saccharum mitochondrial genomes.
... Studies have shown that gene transfer occurs between chloroplast, mitochondrial, and nuclear genes (Choi & Park, 2021;Park et al., 2015). In fact, chloroplast gene fragments are found in the mitochondrial genomes of many species, but the migration varies greatly in different species (Y. ...
Poa pratensis is a widely cultivated turf grass with strong cold and drought resistance. While the chloroplast genome of P. pratensis has been sequenced, its mitochondrial genome remains unexplored. This study assembled the mitochondrial genome of P. pratensis, revealing a total length of 447,463 bp and a guanine‐cytosine content of 44.41%. Its main structure comprises a single circular molecule. Annotation results revealed the presence of 56 genes, including 34 unique protein‐coding genes, 19 tRNA genes, and three rRNA genes. Additionally, we investigated codon usage bias, repeats, sequence migration, and RNA editing events in the genome. Furthermore, we constructed a phylogenetic tree based on the mitochondrial genomes of P. pratensis and 20 related plants. Notably, synteny analysis results demonstrated that the mitochondrial genome of P. pratensis exhibited greater variation and more significant rearrangement than those of its close relatives. This study reports the complete mitochondrial genome of P. pratensis for the first time, providing a solid foundation for further research into the genetics of bluegrass.
... Lastly, certain plant mitochondrial genomes have incorporated genes via the gene transfer from different species. This phenomenon is quite prevalent in angiospermae, especially from its chloroplast neighbors, to obtain several plastid sequences, this process lasted a long time and is likely continuing [22][23][24]. ...
Background
Santalum album L. is an evergreen tree which is mainly distributes throughout tropical and temperate regions. And it has a great medicinal and economic value.
Results
In this study, the complete mitochondrial genome (mitochondrial genome) of S. album were assembled and annotated, which could be described by a complex branched structure consisting of three contigs. The lengths of these three contigs are 165,122 bp, 93,430 bp and 92,491 bp. We annotated 34 genes coding for proteins (PCGs), 26 tRNA genes, and 4 rRNA genes. The analysis of repeated elements shows that there are 89 SSRs and 242 pairs of dispersed repeats in S. album mitochondrial genome. Also we found 20 MTPTs among the chloroplast and mitochondria. The 20 MTPTs sequences span a combined length of 22,353 bp, making up 15.52% of the plastome, 6.37% of the mitochondrial genome. Additionally, by using the Deepred-mt tool, we found 628 RNA editing sites in 34 PCGs. Moreover, significant genomic rearrangement is observed between S. album and its associated mitochondrial genomes. Finally, based on mitochondrial genome PCGs, we deduced the phylogenetic ties between S. album and other angiosperms.
Conclusions
We reported the mitochondrial genome from Santalales for the first time, which provides a crucial genetic resource for our study of the evolution of mitochondrial genome.
