The mitochondrial genome of soybean reveals complex genome structures and gene evolution at intercellular and phylogenetic levels.

Shengxin Chang,Junyi Gai,Tuanjie Zhao,Rongzhan Guan,Jijie Li,Yankun Wang,Jiangjie Lu,Pu Chu,Ying Xu

doi:10.1371/journal.pone.0056502

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.

Highlights

The size of the mitochondrial genome in seed plants is highly variable [1,2], ranging from 208 kb in white mustard [3] to 11.3 Mb in Silene conica [4]
15,861 reads covering 6,317,283 bp were generated, and the data were assembled into 33 contigs. Searching with these contigs against the reported nuclear and chloroplast genomes of soybean [22,23] showed that five of the contigs (,500 bp) that had low sequencing coverage depths of 3–4 are contaminant DNAs: three are nuclear genome sequences and two are chloroplast genome sequences. These sequences were removed from the assembly of the soybean mitochondrial genome
Components of the Soybean Mitochondrial Genome The size of the soybean mitochondrial genome is moderate relatively to the small Brassica mitochondrial genomes, which are mostly less than 300 kb [13,17,28]

Summary

Introduction

The size of the mitochondrial genome (mtDNA) in seed plants is highly variable [1,2], ranging from 208 kb in white mustard [3] to 11.3 Mb in Silene conica [4]. Mitochondrial genomes in seed plants are enriched with repeats, such as tandem repeats, short repeats and large repeats [6,7,8]. The large repeats, usually larger than 1 kb, may mediate reversible recombination of the mitochondrial genomes, regulate the molecular conformation of the genome, and may reflect or predict the possible constituents of the genome molecular pools that function in energy metabolism of plants [11]. The smallest mitochondrial genome (white mustard) does not have any large repeats [3]

Methods

Results

Conclusion