Comparative chloroplast genome analyses of DC. species: new insights into genome evolution and phylogenomic implications.

The genus DC. comprises about 310 species distributed in Asia, Europe, and North America. Previous studies based on evidences from morphology or a few molecular markers are helpful for understanding the classification and systematic evolution of . However, a scarcity of chloroplast genomic resources for has hindered the understanding of the genus's systematic classification and chloroplast genome evolution. Here comparative genomic analyses were conducted on chloroplast genomes of 24 species. Chloroplast genomes of species showed the triad structure due to the loss of one copy of the IR, with the size range from 121854 bp to 125271 bp. The cp genomes encoded a total of 110 genes, including 76 protein-coding genes (PCGs), 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. It was found that the intron, one intron, one intron, gene, gene, and gene were lost in the cp genomes. Seven regions ( intron, , , ) were chosen as potential molecular markers, which will contribute to species identification, population genetics and phylogenetic studies of The phylogenetic relationships among species provided some implications for the classification of . Congruent with studies based on the morphological evidence, the close relationships between and , as well as and were revealed. The results supported the treatment of as a separate species and refuted the inclusion of in as conspecific taxa. In addition, it was suggested that should be considered as a separate species rather than its inclusion in . The 16 positively selected genes (, , , , , , , , , , , , ) are related to important biological processes for instance self-replication, photosynthesis and metabolite biosynthesis, which may contribute to the adaptation of to its habitats. This study will lay a solid foundation for further studies on species identification, taxonomy, and systematic evolution of .