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Background  As one of the largest genera in Apiaceae,  Bupleurum  L. is well known for its high medicinal value. The genus has frequently attracted the attention of evolutionary biologist and taxonomist for its distinctive characteristics in the Apiaceae family. Although some chloroplast genomes data have been now available, the changes in the structure of chloroplast genomes and selective pressure in the genus have not been fully understood. In addition, few of the species are endemic to Southwest China, a distribution and diversity center of Chinese  Bupleurum . Endemic species are key components of biodiversity and ecosystems, and investigation of the chloroplast genomes features of endemic species in  Bupleurum  will be helpful to develop a better understanding of evolutionary process and phylogeny of the genus. In this study, we analyzed the sequences of whole chloroplast genomes of 4 Southwest China endemic  Bupleurum  species in comparison with the published data of 17  Bupleurum  species to determine the evolutionary characteristics of the genus and the phylogenetic relationships of Asian  Bupleurum .    Results  The complete chloroplast genome sequences of the 4 endemic  Bupleurum  species are 155,025 bp to 155,323 bp in length including a SSC and a LSC region separated by a pair of IRs. Comparative analysis revealed an identical chloroplast gene content across the 21  Bupleurum  species, including a total of 114 unique genes (30 tRNA genes, 4 rRNA genes and 80 protein-coding genes). Chloroplast genomes of the 21  Bupleurum  species showed no rearrangements and a high sequence identity (96.4–99.2%). They also shared a similar tendency of SDRs and SSRs, but differed in number (59–83). In spite of their high conservation, they contained some mutational hotspots, which can be potentially exploited as high-resolution DNA barcodes for species discrimination. Selective pressure analysis showed that four genes were under positive selection. Phylogenetic analysis revealed that the 21  Bupleurum  formed two major clades, which are likely to correspond to their geographical distribution.    Conclusions  The chloroplast genome data of the four endemic  Bupleurum  species provide important insights into the characteristics and evolution of chloroplast genomes of this genu, and the phylogeny of  Bupleurum .    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-08008-z.

bmc genomics

The chloroplast genomes of four Bupleurum (Apiaceae) species endemic to Southwestern China, a diversity center of the genus, as well as their evolutionary implications and phylogenetic inferences