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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.

Comparative analysis of complete plastid genomes from wild soybean (Glycine soja) and nine other Glycine species