Correction: 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 Genome Analysis of Wild Rice (Oryza minuta) and Its Comparison with Other Related Species

“…Among them, six genes exhibited high sequence similarity (>99%) to the chloroplast genome and seemed to be derived from the chloroplast. The chloroplast-derived genes ( trnW-CCA , trnD-GUC , trnS-GGA , trnH-GTG , trnM-CAT and trnL-CAA) , which are commonly found in angiosperm mitochondrial genomes [ 51 ], were present in the O . minuta mitogenome.…”

The Multipartite Mitochondrial Genome of Marama (Tylosema esculentum)

“…The total length of the marama mitochondrial genome is 399,572 bp, which is slightly shorter than the mitochondrial genomes of some other Fabaceae, 402,558 bp for Glycine max , 401,262 bp for Vigna radiate and 425,718 bp for Millettia pinnata ( Alverson et al, 2011 ; Kazakoff et al, 2012 ; Chang et al, 2013 ; Negruk, 2013 ), but larger than Arabidopsis thaliana (366,924 bp) ( Unseld et al, 1997 ). The GC content is 44.71%, close to 44.8% of Arabidopsis thaliana ( Unseld et al, 1997 ), 45.4% of Millettia pinnata ( Kazakoff et al, 2012 ), and 45.1% of Vigna radiata ( Alverson et al, 2011 ).…”

“…12 long contigs were obtained from the direct assembly of PacBio reads using Canu v2.2 and the contigs were aligned to the structure units of LS1 and LS2 using BLAST to verify the connections as shown in Supplementary Figures 6 – 17 . However, whether they can further combine to form one large circular molecule like the mtDNA of other legumes including Millettia pinnata , Vigna radiate , and Glycine max ( Alverson et al, 2011 ; Kazakoff et al, 2012 ; Chang et al, 2013 ) in other marama individuals still needs to be determined. In addition, from the PacBio data, the ratio of five basic rings to the two large molecules was found to be approximately 1:1 ( Figure 2 ), but the sample size is very small and more PacBio data or qPCR amplifications at the junctions are required to verify the ratios.…”

“…Genes including nad1 , nad2 , nad4 , nad5 , nad7 , and ccmFc contain introns as shown in Figure 4 . The tRNA gene trnfM-CAT has two copies in the marama mitochondrial genome, while it has four copies in the mitogenomes of soybean ( Chang et al, 2013 ). Some genes have been lost during angiosperm evolution ( Table 4 ).…”

“…For example, rpl10 is absent from the mitochondrial genomes of Millettia pinnata and Vigna radiata , however, it is present and functional in marama ( Alverson et al, 2011 ; Kazakoff et al, 2012 ). Genes including cox2 and rps1 are missing from the mtDNA of Vigna radiata and Lotus japonicus , but remain intact in marama, Millettia pinnata , and Glycine max mtDNA ( Kazakoff et al, 2012 ; Chang et al, 2013 ). sdh4 exists as a pseudogene in Millettia pinnata and soybean, but it was found to be functional in the mitogenome of marama ( Kazakoff et al, 2012 ; Chang et al, 2013 ).…”