The Mitochondrial Genome of Soybean Reveals Complex Genome Structures and Gene Evolution at Intercellular and Phylogenetic Levels

Abstract

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 with its nuclear and chloroplast genomes. The present study helps to solve a 30-year mystery regarding the most complex mitochondrial genome structure, showing that pairwise rearrangements among the many large repeats may produce an enriched molecular pool of 760 circles in seed plants. The soybean mitochondrial genome harbors 58 genes of known function in addition to 52 predicted open reading frames of unknown function. The genome contains sequences of multiple identifiable origins, including 6.8 kb and 7.1 kb DNA fragments that have been transferred from the nuclear and chloroplast genomes, respectively, and some horizontal DNA transfers. The soybean mitochondrial genome has lost 16 genes, including nine protein-coding genes and seven tRNA genes; however, it has acquired five chloroplast-derived genes during evolution. Four tRNA genes, common among the three genomes, are derived from the chloroplast. Sizeable DNA transfers to the nucleus, with pericentromeric regions as hotspots, are observed, including DNA transfers of 125.0 kb and 151.6 kb identified unambiguously from the soybean mitochondrial and chloroplast genomes, respectively. The soybean nuclear genome has acquired five genes from its mitochondrial genome. These results provide biological insights into the mitochondrial genome of seed plants, and are especially helpful for deciphering vital activities in soybean.

Mitochondrial SSRs and their utility in distinguishing wild species, CMS lines and maintainer lines in pigeonpea (Cajanus cajan L.)

“…The frequency of SSRs in pigeonpea mitochondrial genome observed during the present study was relatively low, when compared with that in mitochondrial genomes of cereals (Rajendrakumar et al 2007(Rajendrakumar et al , 2008. In the case of legumes other than pigeonpea, the mitochondrial genomes of mung bean (Vigna radiata) (Alverson et al 2011), faba bean (Negruk 2013) and soybean (Chang et al 2013) have been sequenced. However, SSRs in the mitochondrial genomes of these above other legumes have yet to be discovered.…”

Analysis of nuclear mitochondrial DNAs and factors affecting patterns of integration in plant species

“…Although both nuclear and mitochondrial genomic sequences of Ricinus communis have been reported (Chan et al, 2010;Rivarola et al, 2011), a preliminary inspection revealed that the assembly status of the nuclear genome was inadequate for analysis of NUMTs, and thus we excluded it from the current study. The species used were as follows: Arabidopsis thaliana (Giegé and Brennicke et al, 1999;Arabidopsis Genome Initiative, 2000), Carica papaya (Rice et al, unpublished NC_012116;Ming et al, 2008), Vitis vinifera (French-Italian Public Consortium for Grapevine Genome Characterization, 2007;Goremykin et al, 2009), Lotus japonicus (Sato et al, 2008;Kazakoff et al, 2012), Glycine max (Schmutz et al, 2010;Chang et al, 2013), Cucumis sativus (Huang et al, 2009;Alverson et al, 2011b), Oryza sativa (Notsu et al, 2002;International Rice Genome Sequencing Project, 2005), Sorghum bicolor (Allen et al, unpublished NC_008360;Paterson et al, 2009), and Zea mays (Clifton et al, 2004;Schnable et al, 2009). The nine species include six eudicots and three monocots (all Gramineae).…”

Organellar Genomes of Flowering Plants

“…Similarly, large inverted repeats in mitochondrial genome may also recombine to give rise to isometric genome structures. Both the isometric and sub-circular forms are subgenomic structural isomeric forms of the master circle genome (Chang et al 2013 ). Sometimes, illegitimate recombination may occur at short repeat sequences that give rise to substoichiometric DNA molecules called sublimons.…”