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![The circular map of the mitochondrial genome of G. max. Features on the clockwise-and counter-clockwise-transcribed strands are drawn on the inside and outside of the circle, respectively. The figure was drawn using OGDraw v1.2 [65]. doi:10.1371/journal.pone.0056502.g001](profile/Pu-Chu-2/publication/235691925/figure/fig10/AS:669665818845201@1536672181554/The-circular-map-of-the-mitochondrial-genome-of-G-max-Features-on-the-clockwise-and.jpg)
The circular map of the mitochondrial genome of G. max. Features on the clockwise-and counter-clockwise-transcribed strands are drawn on the inside and outside of the circle, respectively. The figure was drawn using OGDraw v1.2 [65]. doi:10.1371/journal.pone.0056502.g001
Source publication
Determining mitochondrial genomes is important for elucidating vital activities of seed plants. Mitochondrial genomes are specific to each plant species because of their variable size, complex structures and patterns of gene losses and gains during evolution. This complexity has made research on the soybean mitochondrial genome difficult compared w...
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... bb.454contignet software was used to join the contigs and obtain a connecting map. To verify the 36 connections of contigs, we designed correspond- ing primers (Table S1 in File S1) and the expected bands were obtained for all 36 primer sets ( Figure S1). Sanger sequencing was then applied to verify the assembly. ...
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... of known function account for 18.2% of the whole genome (Table S2 in File S1). The positions of these genes in the soybean mitochondrial genome are shown in Figure 1. Among genes of known function, nad4L and atp6 are present in two copies, atp1 has three copies, there are three copies of the fifth exon of nad7, and trnfM-CAT has four copies. ...
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... large repeats in the same orientation may produce two small subgenomic circles [7,12]. For example, the soybean genome in Figure 3A (the same as Figure 1) may produce two subgenomic circles comprising a large subgenomic circle of 322,625 bp and a small subgenomic circle of 79,933 bp, mediated by the pairwise large repeats R1b and R1d ( Figure 3B). The large subgenomic circle may further produce two smaller circles of 98,721 bp and 223,904 bp, mediated by another pair of large repeats (R1d and R1e) that are present in this large subgenomic circle ( Figure 3C). ...
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... pairs of large repeats in the reverse direction may mediate the formation of isometric mitochondrial genome circles equiva- lent to the master circle shown in Figure 1 and 3A [7,12]. The sequence obtained has eight pairs of reversed large repeats; therefore, the genome has eight isometric master circular genomic structures ( Figure 4B-I). ...
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... analysis of the intercellular DNA transfer in soybean is summarized in Figure 8: (1) The DNA segments transferred from the chloroplast and mitochondrial genomes into the nucleus are very large (.120 kb); (2) The transfer from the nucleus to the mitochondria is ambiguous because of the difficulty in determining the orientation of the transfers, except for small amounts of DNA sequences with vestiges of nuclear transposons (6.8 kb); (3) No DNA transfer was observed from the nucleus to the chloroplast and from the chloroplast to the ...
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... positions included were 1st+2nd+3rd+Noncoding and the number of bootstrap replications was set as 1000. Figure S1 Agarose gel electrophoresis of PCR product in Table S1. Figure S3 GC content distribution and sequencing depth distribution of the soybean mitochondrial ge- nome. Top image: GC content (/200 bp) of the soybean mitochondrial genome; Bottom image: sequencing depth distribu- tion (/bp). ...
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Background
Sequencing analysis of mitochondrial genomes is important for understanding the evolution and genome structures of various plant species. Barley is a self-pollinated diploid plant with seven chromosomes comprising a large haploid genome of 5.1 Gbp. Wild barley (Hordeum vulgare ssp. spontaneum) and cultivated barley (H. vulgare ssp. vulga...
Citations
... Undergoing genome replication, frequent homologous recombination, gene loss or transfer to the plastome or nuclear genome, and the conformation and size of plant mitogenome between different lineages are variable [13,14]. Most of the plant mitogenome assembled displayed as a single circular map reported in some plants, including Arabidopsis thaliana (L.) Heynh., Suaeda glauca (Bunge) Bunge., zucchini, and some crops [15][16][17][18][19][20]. A few cases exist where the mitogenomes are linear DNA molecules or linear-circular combinations, as evidenced in rice and spearmint [21,22]. ...
The Plateau Hongliu (Myricaria elegans Royle.) is a woody shrub halophyte that thrives in arid areas of western Tibet, the Himalayan Mountains. It is acclaimed as superior in saline stress acclimation and as a critical pharmaceutical resource of the Tibetan traditional herb. Nevertheless, the mitogenome in the genus Myricaria remains unknown. Here, using the Illumina and PacBio sequencing assays, the first complete mitogenome of the M. elegans revealed a multi-branched skeleton with a total length of 416,354 bp and GC content of 44.33%, comprising two circular molecules (M1 and 2). The complete mitogenome annotates 31 unique protein-encoding genes (PEGs), fifteen tRNAs, and three rRNA genes. The UAA exhibits the most prominent codon us-age preference as a termination, followed by UUA codons for leucine. The mitogenome contains 99 simple sequence repeats and 353 pairs of dispersed repeats, displaying the most frequent in palindromic repeats. Gene transfer analyses identified 8,438 bp of 18 homologous fragments from the plastome, accounting for 2.03 % of the total length. Using the PREP suit, 350 C-U RNA editing sites were predicted, of which nad4 and ccmB were on the top frequency. Syntenic and phylogenetic analyses suggested weakly conserved patterns of M. elegans in Caryophyllales owing to the genome rearrangement. In summary, the deciphered unique features and complexities of the mitogenome in M. elegans provide novel insights into understanding the evolution and biological conservation underlying climate resilience in halophytes.
... Elucidating the structure of plant mt genomes is challenging due to extensive genomic recombinations [36,37]; lost or pseudogenized genes [38]; gene transfer events between mt and nuclear genomes; and their variable sizes and structures [30,39]. Thus, comparing complete mt and cp genomes in plants is key to understanding their organelle genome evolution. ...
Background: Seagrasses are ideal for studying plant adaptation to marine environments. A previous study reported the transfer of lost chloroplast (cp) genes to the nuclear genome. However, it remains unclear whether the lost cp genes were transferred to the mitochondrial (mt) genome.
Result: A divergent evolutionary trajectory was determined between cp and mt genomes across four seagress species. The cp genome exhibited a more stable genome structure, while the mt genome displayed structural diversity. Compared to other monocotyledons, these seagrasses have smaller mt genomes. This study revealed significant gene loss during evolution, including the complete loss of all cp-rpl19 genes in Zosteraceae; most of cp-ndh genes in Hydrocharitaceae; and mt-rpl and mt-rps genes in all seagrasses, except for the mt-rpl16 gene in P. iwatensis. Notably, most ribosomal protein genes were lost in both mt and cp genomes. Horizontal gene transfer showed that the deleted cp genes were not transferred to the mt genome. Extensive sequence transfer between the organelles of the four seagrasses was discovered, with the mt genome of Zostera containing a large portion of DNA transferred from the cp genome. Rearrangement analyses revealed an inversion in the cp genome of R. sinensis, which had not been reported previously. Moreover, four positively selected genes (atp8, nad5, atp4, and ccmFn) and five variable regions (matR, atp4, atp8, rps7, and ccmFn) were identified in seagrasses, potentially associated with their adaptation to the marine environment.
Conclusion: In this study, we assembled and annotated the complete organelle genome of R. sinensis. This study enriches the genomic resources and provides new evidence of dynamic gene evolution in seagrasses.
... Most DNA transfers between chloroplasts and mitochondria are one-way transfers from the cpGenome to the mtGenome (Wang et al., 2007). For instance, four complete genes (trnD-GUC, trnH-GUG, trnN-GUU, and trnW-CCA) participated in HGT in Soybeans (Chang et al., 2013); and multiple ribosomal proteins in the Geranium underwent HGT events (Park et al., 2015). In the mtGenome of Z. mauritiana, we found 10 complete genes that transferred from the cpGenome. ...
Ziziphus mauritiana Lam. is a valuable semi-deciduous tropical fruit tree with economic, medicinal, nutritional, and environmental significance. While the chloroplast genome of Z. mauritiana has been studied, the decoding of its mitochondrial genome (mtGenome) is crucial for various research areas, including molecular phylogeny and functional genomics. In this study, we extracted high-quality genomic DNA from the green leaves of Z. mauritiana and assembled the mtGenome by integrating sequencing data from both long and short reads. The Z. mauritiana mtGenome spans 324,124 bp with a 45.43 % GC content and exhibits six distinct conformations alongside the main circular sequence due to three pairs of repetitive fragments that facilitate recombination. RNA editing events resulted in changes in the physicochemical properties of amino acids, with genes expressed at higher levels showing an increased frequency of editing sites. Chloroplast-to-mitochondria horizontal gene transfers occurred in Z. mauritiana; however, these transferred fragments had few mutations, posing a challenge in determining the exact timing of these transfers. Phylogenetic analysis highlights a slower evolution rate of mitochondrial genes compared to chloroplast genes. These insights greatly enhance our understanding of the dynamics of the Z. mauritiana mtGenome, including recombination, gene expression, evolutionary processes, and more. The data and results of this study will serve as valuable mtGenome data resources within the Rhamnaceae family, thereby facilitating further genomics-based studies on Z. mauritiana.
... The transfer of tRNA gene sequences from chloroplasts to mitochondrial genomes are common in plants (Bergthorsson et al., 2003). Inserted tRNAs accounted for 25% of the total transferred sequences in the P. pedunculata mitogenome, which contradicts the hypothesis that most transferred genes are tRNA genes (Chang et al., 2013). ...
Introduction
Prunus pedunculata (Prunoideae: Rosaceae), a relic shrub with strong resistance and multiple application values, is endangered in China. Extensive research had been devoted to gene expression, molecular markers, plastid genome analysis, and genetic background investigations of P. pedunculata. However, the mitochondrial genome of this species has not been systematically described, owing to the complexity of the plant mitogenome.
Methods
In the present research, the complete mitochondrial genome of P. pedunculata was assembled, annotated, and characterized. The genomic features, gene content and repetitive sequences were analyzed. The genomic variation and phylogenetic analysis have been extensively enumerated.
Results and discussion
The P. pedunculata mitogenome is a circular molecule with a total length of 405,855 bp and a GC content of 45.63%, which are the smallest size and highest GC content among the known Prunus mitochondrial genomes. The mitogenome of P. pedunculata encodes 62 genes, including 34 unique protein-coding genes (PCGs, excluding three possible pseudogenes), three ribosomal RNA genes, and 19 transfer RNA genes. The mitogenome is rich in repetitive sequences, counting 112 simple sequence repeats, 15 tandem repeats, and 50 interspersed repetitive sequences, with a total repeat length of 11,793 bp, accounting for 2.91% of the complete genome. Leucine (Leu) was a predominant amino acid in PCGs, with a frequency of 10.67%, whereas cysteine (Cys) and tryptophan (Trp) were the least adopted. The most frequently used codon was UUU (Phe), with a relative synonymous codon usage (RSCU) value of 1.12. Selective pressure was calculated based on 20 shared PCGs in the mitogenomes of the 32 species, most of which were subjected to purifying selection (Ka/Ks < 1), whereas ccmC and ccmFn underwent positive selection. A total of 262 potential RNA editing sites in 26 PCGs were identified. Furthermore, 56 chloroplast-derived fragments were ascertained in the mitogenome, ranging from 30 to 858 bp, and were mainly located across IGS (intergenic spacer) regions or rRNA genes. These findings verify the occurrence of intracellular gene transfer events from the chloroplast to the mitochondria. Furthermore, the phylogenetic relationship of P. pedunculata was supported by the mitogenome data of 30 other taxa of the Rosaceae family. Understanding the mitochondrial genome characteristics of P. pedunculata is of great importance to promote comprehension of its genetic background and this study provides a basis for the genetic breeding of Prunus.
... The integration of DNA elements into the mt genome via intracellular and horizontal transfer has been a common phenomenon during plant evolution (Bergthorsson et al. 2005;Ma et al. 2022). As a consequence, plant mt genomes vary considerably in length, gene content, and gene sequence Shengxin et al. 2013). The largest land plant mitogenome is $11.3 Mb (Silene conica) (Sloan et al. 2012), and the smallest is $66 kb (Viscum scurruloideum) (Skippington et al. 2015), but most genomes comprise 200-800 kb (Guo et al. 2016). ...
Ficus carica Linn. is an important economic tree species with high developmental prospects and scientific research for edible and medicinal value. The F. carica chloroplast genome has recently been reported; however, the mitochondrial genome is still unexplored. We assembled the complete mitogenome of F. carica using reads from PacBio Biosciences sequencing platforms. The circular mitogenome F. carica has a length of 480,902 base pairs (bp), which contain 46 genes, including 27 protein-coding genes, 16 transfer RNA (tRNA) genes, and three ribosomal RNA (rRNA) genes. The base composition, codon usage, sequence repeats, RNA editing, and selective pressure were examined. We also conducted the phylogenetic analysis based on the mitogenomes of F. carica and 21 other taxa to know the evolutionary and taxonomic status of F. carica . Our analyses provided comprehensive information on the F. carica mitochondrial genome, which would facilitate evolutionary research in other fruit trees in the future.
... fa:2:30:10 SLIDING-WINDOW:15:30 MINLEN:110 TRAILING:30 AVG-QUAL:30, " followed by removal of reads that could be aligned to the host (Capra hircus, GCF_001704415.1) [34] or food (Zea mays, GCF_000005005.2; Medicago truncatula, GCF_000219495.3 and Glycine max, GCF_000004515.5) [35][36][37] genomes using Bowtie2 (v 2.3.5.1) [38]. Overall, a median of ~ 1.3G bases were removed from each sample. ...
Background
Goat is an important livestock worldwide, which plays an indispensable role in human life by providing meat, milk, fiber, and pelts. Despite recent significant advances in microbiome studies, a comprehensive survey on the goat microbiomes covering gastrointestinal tract (GIT) sites, developmental stages, feeding styles, and geographical factors is still unavailable. Here, we surveyed its multi-kingdom microbial communities using 497 samples from ten sites along the goat GIT.
Results
We reconstructed a goat multi-kingdom microbiome catalog (GMMC) including 4004 bacterial, 71 archaeal, and 7204 viral genomes and annotated over 4,817,256 non-redundant protein-coding genes. We revealed patterns of feeding-driven microbial community dynamics along the goat GIT sites which were likely associated with gastrointestinal food digestion and absorption capabilities and disease risks, and identified an abundance of large intestine-enriched genera involved in plant fiber digestion. We quantified the effects of various factors affecting the distribution and abundance of methane-producing microbes including the GIT site, age, feeding style, and geography, and identified 68 virulent viruses targeting the methane producers via a comprehensive virus-bacterium/archaea interaction network.
Conclusions
Together, our GMMC catalog provides functional insights of the goat GIT microbiota through microbiome-host interactions and paves the way to microbial interventions for better goat and eco-environmental qualities.
-Pdb_6YZpzy_mmd53S_tihVideo Abstract
... The mitogenomes of the Cercidoideae species, T. esculentum and C. canadensis contain functional protein-coding genes sdh3, sdh4, and rpl10, which have been lost in many other legumes (Table 4). Rare gene losses were also seen in the mitogenomes of some legumes, such as rpl5 in G. max, cox2 in V. radiata, and rps1 in L. japonicus, but these genes all remain intact and functional in T. esculentum and C. canadensis [84][85][86]. The loss of mitochondrial protein-coding genes and the functional transfer of these genes from the organelle genome to the nuclear genome are common in the evolution of angiosperms, but some plants tend to retain a more complete set of mitochondrial genes [83]. ...
... The mitogenomes of the Cercidoideae species, T. esculentum and C. canadensis contain functional protein-coding genes sdh3, sdh4, and rpl10, which have been lost in many other legumes (Table 4). Rare gene losses were also seen in the mitogenomes of some legumes, such as rpl5 in G. max, cox2 in V. radiata, and rps1 in L. japonicus, but these genes all remain intact and functional in T. esculentum and C. canadensis [84][85][86]. Table 4. List of mitochondrial protein-coding genes lost during the evolution of some Fabaceae species (+ Present, -Absent). ...
... The type 2 mitogenome contains three circular molecules and one linear chromosome with a total length of 436,568 bp. The size of the assembled marama mitogenomes are close to that of some other legumes, 402.6 kb for G. max, 401.3 kb for V. radiata, 425.7 kb for Pongamia pinnata, and 380.9 kb for L. japonicus [59,85,86]. A mix of linear and circular molecules has also been previously proposed in the mitogenomes of plants such as Lactuca sativa and S. tuberosum [32,39]. ...
Simple Summary
Tylosema esculentum is a potential crop in southern Africa, known for its high nutritional value and ability to thrive in long-term drought conditions. To gain a better understanding of its genetic characteristics, the mitogenomes of 84 individuals from different locations in Namibia and South Africa were assembled and compared using both PacBio and Illumina sequencing data. The study revealed two distinct germplasms with significant differences in the mitogenome structure and sequence. Comparative genomics analysis was conducted to explore heteroplasmy and horizontal transfer in the marama mitogenome, providing valuable insights into cytoplasmic genetic diversity and inheritance. Additionally, evolutionary studies were performed on marama and its related legumes, indicating that the Cercidoideae subfamily tends to possess a more complete set of mitochondrial genes compared to the Faboideae species. The findings made in this study not only contribute to the germplasm selection and future marama breeding but also enhance our understanding of the inheritance and evolution of plant mitogenomes.
Abstract
Tylosema esculentum, commonly known as the marama bean, is an underutilized legume with nutritious seeds, holding potential to enhance food security in southern Africa due to its resilience to prolonged drought and heat. To promote the selection of this agronomically valuable germplasm, this study assembled and compared the mitogenomes of 84 marama individuals, identifying variations in genome structure, single-nucleotide polymorphisms (SNPs), insertions/deletions (indels), heteroplasmy, and horizontal transfer. Two distinct germplasms were identified, and a novel mitogenome structure consisting of three circular molecules and one long linear chromosome was discovered. The structural variation led to an increased copy number of specific genes, nad5, nad9, rrnS, rrn5, trnC, and trnfM. The two mitogenomes also exhibited differences at 230 loci, with only one notable nonsynonymous substitution in the matR gene. Heteroplasmy was concentrated at certain loci on chromosome LS1 (OK638188). Moreover, the marama mitogenome contained an over 9 kb insertion of cpDNA, originating from chloroplast genomes, but had accumulated mutations and lost gene functionality. The evolutionary and comparative genomics analysis indicated that mitogenome divergence in marama might not be solely constrained by geographical factors. Additionally, marama, as a member from the Cercidoideae subfamily, tends to possess a more complete set of mitochondrial genes than Faboideae legumes.
... We investigated the loss of PCGs in eudicots, monocots, gymnosperms, bryophytes, and phycophyta (Fig. 8). Compared to highly variable ribosomal proteins and genes in succinate dehydrogenase, most PCGs are conserved in different plant mitogenomes, especially in the following genes: ATP synthase, cytochrome c biogenesis, ubichinol cytochrome c reductase, cytochrome c oxidase, maturases, transport membrane protein, and NADH dehydrogenase (Chang et al. 2013). To some extent, the conservation of these genes indicates that they play a crucial role in plants' mitochondrial function. ...
Pepper ( Capsicum pubescens ), one of the five domesticated pepper species, boasts unique characteristics such as numerous hairs on the epidermis of its leaves and stems, black seeds, and vibrant purple flowers. Previously, no studies have reported on the complete assembly of the mitochondrial genome (mitogenome) of C. pubescens . Understanding the mitogenome is crucial for further research on C. pubescens . In our study, we successfully assembled the first mitogenome of C. pubescens , which has been assigned the GenBank accession number OP957066. This mitogenome has a length of 454,165 bp and exhibits the typical circular structure observed in most mitogenomes. We have annotated a total of 70 genes, including 35 protein-coding genes (PCGs), 30 tRNA genes, 3 rRNA genes, and 2 pseudogenes. Compared to the other three pepper mitogenomes (KJ865409, KJ865410, and MN196478), C. pubescens OP957066 exhibits 4 unique PCGs ( atp4 , atp8 , mttB , and rps1 ), while 2 PCGs ( rpl10 and rps3 ) are absent. It's worth mentioning that each of the three pepper mitogenomes (KJ865409, KJ865410, and MN196478) experienced the loss of 4 PCGs ( atp4 , atp8 , mttB , and rps1 ). To further explore the evolutionary relationships, we reconstructed a phylogenetic tree using the mitogenomes of C. pubescens and fourteen other species. The structural comparison and synteny analysis of the above four pepper mitogenomes showed that C. pubescens has a higher sequence similarity with KJ865409, and C. pubescens experienced rearrangements with the other three pepper mitogenomes. Interestingly, we observed 72 homologous sequences between the mitochondrial and chloroplast genomes, which accounted for 12.60% of the mitogenome, with a total length of 57,207 bp. These sequences encompassed 12 tRNA genes and the rRNA gene ( rrn18 ). Remarkably, selective pressure analysis suggests that the nad5 gene underwent obvious positive selection. Furthermore, the single base mutation in three genes ( nad1 , nad2 , and nad4 ) resulted in amino acid change. This study has provided a high-quality mitogenome of pepper, offering valuable molecular data for future investigations into the genetic information exchange between organelle genomes in pepper.
... Based on 23 conserved protein-coding genes (atp1, atp4, atp6, atp8, atp9, ccmB, ccmC, cox1, cox3, cytb, matR, mttB, nad1, nad2, nad3, nad4, nad5, nad6, nad7, rpl2, rps10, rps19, rps3) in the mitochondrial genomes, the phylogenetic analysis showed that 24 plants were divided into five branches. The following sequences with GenBank accession were used: Glycine max NC_020455 (Chang et al. 2013 The numbers above the branches were the bootstrap value. The 23 conserved protein-coding genes (atp1, atp4, atp6, atp8, atp9, ccmB, ccmC, cox1, cox3, cytb, matR, mttB, nad1, nad2, nad3, nad4, nad5, nad6, nad7, rpl2, rps10, rps19, rps3) in the mitochondrial genomes were used to construct the phylogenetic. ...
The mitochondrial genome of Camellia nitidissima was sequenced by Illumina and Pacbio sequencing. The results of sequences showed that a total length was 949,915 bp, and the GC content was 45.7% in assembled mitochondrial genome of C. nitidissima. 71 unigenes had been found, including 36 coding proteins and 35 non-coding proteins. Subsequently, the phylogenetic tree was built on 24 plants with the maximum-likelihood method, which had high bootstrap value and fited to the angiosperm phylogeny group classification (APG IV). The study’s findings unravel the taxonomic status of C. nitidissima and benefit the evolution study.
... The 385 mitogenomes of Cercidoideae species T. esculentum and C. canadensis contain functional 386 protein-coding genes sdh3, sdh4, and rpl10, which have been lost in many other legumes (Table 387 4). Rare gene losses were also seen in the mitogenomes of legumes, such as rpl5 in G. max, cox2 388 in V. radiata and rps1 in L. japonicus, but these genes all remain intact and functional in T. 389 esculentum and C. canadensis (Alverson et al., 2011;Kazakoff et al., 2012;Chang et al., 2013). ...
Tylosema esculentum (marama bean), an underutilized legume with edible and nutritious seeds, has the potential to improve local food security in southern Africa. This study investigated the diversity of marama mitogenomes by mapping sequencing data from 84 individuals to the previously published reference mitogenome. Two distinct germplasms were found, and a new mitogenome structure containing three circular molecules and one long linear chromosome was identified, with a unique 2,108 bp fragment and primers were designed on that for marama mitogenome typing. This structural variation increases copy number of certain genes, including nad9 , rrns and rrn5 . The two mitogenomes also differed at 230 loci, with only one nonsynonymous substitution in matR . The evolutionary analysis suggested that the divergence of marama mitogenomes may be related to soil moisture level. Heteroplasmy in the marama mitogenome was concentrated at specific loci, including 127,684 bp to 127,686 bp on chromosome LS1 (OK638188), and may be crucial in the evolution. Additionally, the mitogenomes of marama contained a cpDNA insertion of over 9 kb with numerous polymorphisms, resulting in the loss of function of the genes on that segment. This comprehensive analysis of marama mitogenome diversity may provide valuable insight for future improvement of the bean.
Highlight
The analysis of 84 marama mitogenomes revealed two germplasms and the structural variation affects certain gene copy numbers. Soil moisture levels may have played important roles in the mitogenome divergence.
