Comparative Chloroplast Genomes of Species: Sequence Divergence and Phylogenetic Relationships.

Sorghum comprises 31 species that exhibit considerable morphological and ecological diversity. The phylogenetic relationships among S species still remain unresolved due to lower information on the traditional DNA markers, which provides a limited resolution for identifying species. In this study, we sequenced the complete chloroplast genomes of and and analyzed the published chloroplast genomes of and to retrieve valuable chloroplast molecular resources for . The chloroplast genomes ranged in length from 140,629 to 140,755 bp, and their gene contents, gene orders, and GC contents were similar to those for other Poaceae species but were slightly different in the number of SSRs. Comparative analyses among the four chloroplast genomes revealed 651 variable sites, 137 indels, and nine small inversions. Four highly divergent DNA regions (, , , and ), which were suitable for phylogenetic and species identification, were detected in the chloroplast genomes. A phylogenetic analysis strongly supported that is a monophyletic group in the tribe Andropogoneae. Overall, the genomic resources in this study could provide potential molecular markers for phylogeny and species identification in .