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

Abstract

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.

Keywords: Bupleurum; Chloroplast genome; Comparative analysis; Phylogenetic analyses.

Fig. 1

Chloroplast genome map of the four Bupleurum species. Genes shown outside of the larger circle are transcribed clockwise, while genes shown inside are transcribed counterclockwise. Thick lines of the smaller circle indicate IRs and the inner circle represents the GC variation across the genic regions

Fig. 2

MAUVE alignment of 21 Bupleurum species chloroplast genomes using Geneious. Within each of the alignments, local collinear blocks are represented by blocks of the same color and linked

Fig. 3

Comparison of the LSC, SSC and IR junction among the 21 Bupleurum cp genomes

Fig. 4

Pairwise Ka/Ks ratios in Bupleurum. This heatmap shows pairwise Ka/Ks ratios between every sequence in the multigene nucleotide alignment. The original satellite imagery was obtained from Google Maps (Map data: Google, TerraMetrics; https://maps.google.com/), and modified with Adobe Illustrator CS6 (Adobe Systems Incorporated, San Jose, CA, USA)

Fig. 5

Molecular phylogenetic trees of 21 Bupleurum and 2 Chamaesium constructed by Maximum likelihood (left) and Bayesian inference (right) analysis based on 80 coding genes. Bootstrap support values (> 50%) based on maximum-likelihood (ML) and posterior probabilities analysis are labelled at each node