Complete Chloroplast Genomes Provide Insights Into Evolution and Phylogeny of (Fabaceae).

The genus Bunge (Desmodieae, Papilionoideae) comprises about 37 species distributed in temperate and tropical Asia. Despite the great potential in soil conservation, horticulture, and medicine usage, little is known about the evolutionary history and phylogenetic relationships of due to insufficient genetic resources. Here, we sequenced and assembled 21 complete chloroplast genomes of species. In combination with the previously published chloroplast genomes of and closely related species, we conducted comparative genomics and phylogenomic analysis on these data. Comparative analysis of the genome size, structure, expansion and contraction of inverted repeat (IR) boundaries, number of genes, GC content, and pattern of simple sequence repeats (SSRs) revealed high similarities among the chloroplast genomes. The activities of long sequence repeats contributed to the variation in genome size and gene content in chloroplast genomes. The chloroplast genomes showed moderate sequence variation, and 13 highly variable regions were identified for species identification and further phylogenetic studies. We also reported one more case of pseudogene in the legume family. The phylogenetic analysis confirmed the monophyly of and the sister relationship between and , the latter two genera were then sister to . The intrageneric relationships of based on genomic scale data were firstly reported in this study. The two positively selected genes ( and ) and eight fast-evolving genes identified in this study may help us to understand the adaptation of species. Overall, this study enhances our understanding of the chloroplast genome evolution and phylogenetic relationships of .