Phylogenetic relationship and comparative analysis of the main Bupleuri Radix species in China.

Background: Bupleuri Radix (Chaihu) is a famous traditional Chinese medicine derived from , Apiaceae. The origin of cultivated Chaihu germplasm in China is unclear, which has led to unstable Chaihu quality. In this study, we reconstructed the phylogeny of the main Chaihu germplasm species in China and identified potential molecular markers to authenticate its origin.

Methods: Three species (eight individuals), , , and , were selected for genome skimming. Published genomes from and var. were used for comparative analysis.

Results: Sequences of the complete plastid genomes were conserved with 113 identical genes ranging from 155,540 to 155,866 bp in length. Phylogenetic reconstruction based on complete plastid genomes resolved intrageneric relationships of the five species with high support. Conflicts between the plastid and nuclear phylogenies were observed, which were mainly ascribed to introgressive hybridization. Comparative analysis showed that noncoding regions of the plastomes had most of the variable sequences. Eight regions (F-H, N-M, 16-K, A-J, C-V/UAC and 1) had high divergence values in species and could be promising DNA barcodes for Chaihu authentication. A total of seven polymorphic cpSSRs and 438 polymorphic nSSRs were detected across the five Chaihu germplasms. Three photosynthesis-related genes were under positive selection, of which D reflected the adaptation fingerprint of to different ecological habitats. Our study provides valuable genetic information for phylogenetic investigation, germplasm authentication, and molecular breeding of Chaihu species.