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

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.

Complete Plastid Genome Sequencing of Eight Species from Hansenia, Haplosphaera and Sinodielsia (Apiaceae): Comparative Analyses and Phylogenetic Implications

“…Not surprisingly, Hansenia is more closely related to Haplosphaera but distantly related to Sinodielsia, which has also been confirmed by nrITS sequences and transcriptome data [8,20]. A collective analysis of our results and previous studies [26][27][28][29] found that the lengths of rps19 and trnH genes entering IRs are usually stable in the same genus or phylogenetically related groups. For example, the length of rps19 gene entering IRs is 57-96 bp in Chamaesium species [27], and 49-84 bp in Bupleurum species [26], which are the phylogenetically basal groups in the Chamaesium clade and Bupleureae.…”

“…Higher GC content (42.7-42.8%) was detected in the IR regions compared to the average of a whole genome, which was possibly due to the presence of rRNA sequences with high GC content (55.2-55.3%) in IR regions. Similarly, the high GC content of rRNA sequences also occurs in other Apiaceae species [26,27]. The ten new plastid genomes contained 133 genes, including eight rRNA, 37 tRNA and 85 protein-coding genes (PCGs) ( Table 2).…”

“…Four pseudogenes-ψrps19, ψycf1 and two ψycf15-were found in all the ten genomes. In comparison, Hansenia, Haplosphaera, Sinodielsia, Bupleurum [26] and Chamaesium [27] plastid genes are consistent in their total number of predicted coding regions.…”

“…Additionally, six genes (atpA, atpB, atpE, atpF, atpH and atpI) of ATP synthase subunits were detected. These PCGs were also detected in Bupleurum [26] and Chamaesium species [27] and are generally involved in the important process of plant growth.…”

“…mairei, Erodium species, Pisum sativum and Vicia faba [21,24,25], which may lead to a reduction in the number of duplicated genes and the length of whole plastid genomes. In Apiaceae, the IRa and IRb were both present in the studied plastid genomes from GenBank, Bupleurum species [26] and Chamaesium species [27] ranging from 26,280-26,303 bp and 25,727-26,147 bp, respectively, and the difference of length is mainly caused by the loss or insertion of the spacer regions. The Hansenia, Haplosphaera and Sinodielsia plastid genomes had almost identical GC content (37.5-37.7%) to whole plastid genomes.…”