Abstract
The plastid genomes of different plant species exhibit significant variation, thereby providing valuable markers for exploring evolutionary relationships and population genetics. Glycine soja (wild soybean) is recognized as the wild ancestor of cultivated soybean (G. max), representing a valuable genetic resource for soybean breeding programmes. In the present study, the complete plastid genome of G. soja was sequenced using Illumina paired-end sequencing and then compared it for the first time with previously reported plastid genome sequences from nine other Glycine species. The G. soja plastid genome was 152,224 bp in length and possessed a typical quadripartite structure, consisting of a pair of inverted repeats (IRa/IRb; 25,574 bp) separated by small (178,963 bp) and large (83,181 bp) single-copy regions, with a 51-kb inversion in the large single-copy region. The genome encoded 134 genes, including 87 protein-coding genes, eight ribosomal RNA genes, and 39 transfer RNA genes, and possessed 204 randomly distributed microsatellites, including 15 forward, 25 tandem, and 34 palindromic repeats. Whole-plastid genome comparisons revealed an overall high degree of sequence similarity between G. max and G. gracilis and some divergence in the intergenic spacers of other species. Greater numbers of indels and SNP substitutions were observed compared with G. cyrtoloba. The sequence of the accD gene from G. soja was highly divergent from those of the other species except for G. max and G. gracilis. Phylogenomic analyses of the complete plastid genomes and 76 shared genes yielded an identical topology and indicated that G. soja is closely related to G. max and G. gracilis. The complete G. soja genome sequenced in the present study is a valuable resource for investigating the population and evolutionary genetics of Glycine species and can be used to identify related species.
Highlights
The chloroplast is a key organelle in photosynthesis and in the biosynthesis of fatty acids, starches, amino acids, and pigments [1, 2]
The assembled G. soja plastome of was typical of angiosperms, with a pair of inverted repeats (IRs) regions (25,574 bp), an large-single-copy region (LSC) of 83,181 bp, and an small single-copy region (SSC) of 178,963 bp (Fig 1); a total size of 152,224 bp; and a GC content of 35.4% (Table 1)
As observed in other angiosperm plastomes, the GC content was unequally distributed in the G. soja plastome; it was high in the IR regions (41.8%), moderate in the LSC region (32.8%), and low in the SSC region (28.73%; Table 1)
Summary
The chloroplast (cp) is a key organelle in photosynthesis and in the biosynthesis of fatty acids, starches, amino acids, and pigments [1, 2]. The plastomes of several members of the Papilionoideae exhibit significant variation and rearrangement, including the loss of an IR region [15] and inversion of a 50-kb portion of the LSC [16, 17]. These features, as well as the loss of introns from the rps and clpP genes [18, 19] and transfer of rpl to the nucleus [20, 21], have been well documented, and their occurrence has been mapped onto the phylogeny of Leguminosae [19]. The complete plastome of G. soja was sequenced (GenBank accession number: KY241814) with the aim of elucidating global patterns of structural variation in the G. soja plastome and comparing it for the first time with the available plastomes of nine other Glycine species (G. max, G. gracilis, G. canescens, G. cyrtoloba, G. dolichocarpa, G. falcata, G. stenophita, G. syndetika, and G. tomentella)
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