Comparative Analysis of the Complete Plastid Genome of Five Bupleurum Species and New Insights into DNA Barcoding and Phylogenetic Relationship.

Jun Li,Zhen-Ying Zheng,Deng-Feng Xie,Song-Dong Zhou,Xian-Lin Guo,Xing-Jin He

doi:10.3390/plants9040543

Abstract

Bupleurum L. (Apiaceae) is a perennial and herbal genus, most species of which have high medicinal value. However, few studies have been performed using plastome data in this genus, and the phylogenetic relationships have always been controversial. In this study, the plastid genomes of Bupleurum chinense and Bupleurum commelynoideum were sequenced, and their gene content, order, and structure were counted and analyzed. The only three published Bupleurum species (B. boissieuanum, B. falcatum, and B. latissimum) and other fifteen allied species were selected to conduct a series of comparative and phylogenetic analyses. The genomes of B. chinense and B. commelynoideum were 155,869 and 155,629 bp in length, respectively, both of which had a typical quadripartite structure. The genome length, structure, guanine and cytosine (GC) content, and gene distribution were highly similar to the other three Bupleurum species. The five Bupleurum species had nearly the same codon usages, and eight regions (petN-psbM, rbcL-accD, ccsA-ndhD, trnK(UUU)-rps16, rpl32-trnL(UAG)-ccsA, petA-psbJ, ndhF-rpl32, and trnP(UGG)-psaJ-rpl33) were found to possess relatively higher nucleotide diversity, which may be the promising DNA barcodes in Bupleurum. Phylogenetic analysis revealed that all Bupleurum species clustered into a monophyletic clade with high bootstrap support and diverged after the Chamaesium clade. Overall, our study provides new insights into DNA barcoding and phylogenetic relationship between Bupleurum and its related genera, and will facilitate the population genomics, conservation genetics, and phylogenetics of Bupleurum in Apiaceae.

Highlights

Bupleurum L. (Apiaceae) is a large genus in Apiaceae, most species of which are perennial herbs
Typical plastid genomes have a quadripartite structure consisting of a small single-copy region (SSC) and a large single-copy (LSC) region jointed by a pair of inverted repeats (IRa and IRb)
The sequences of B. chinense and B. commelynoideum were 155,869 bp and 155,629 bp, respectively, both of which were found to have a typical quadripartite structure comprising a small single-copy region (SSC) and a large single-copy (LSC) region jointed by a pair of inverted repeats (IRa and IRb)

Summary

Introduction

Bupleurum L. (Apiaceae) is a large genus in Apiaceae, most species of which are perennial herbs. The genus contains about 180 species widely distributed in temperate and subtropical of the northern hemisphere, with 42 species (22 endemics) in China [1]. Most Bupleurum plants have high medicinal value and are widely used as a traditional medicine in Asia, Europe, and northern Africa [2]. The mixed usage of different Bupleurum species may bring adverse reactions due to the unawareness of the chemical component [8,9]. Molecular phylogenetic studies based on nuclear ribosomal internal transcribed spacer (nrITS) and plastid DNA introns (rpl and rps16) supported a basal position of the genus Bupleurum within subfamily Apioideae, and considered this genus a distinct tribe [10,11].

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Results

Conclusion