Dataset Information

Complete chloroplast genome and phylogenetic analysis of Bupleurum kaoi Liu, Chao, and Chuang, 1977: an endemic species in Taiwan.

ABSTRACT: Bupleurum kaoi Liu, Chao, and Chuang is an endemic and endangered herb in Taiwan. In this study, the complete circular chloroplast genome of B. kaoi was reconstructed and annotated using Illumina sequencing. The genome size of B. kaoi is 155,938 bp, including a pair of inverted repeat regions (IRs: 26308 bp), separated by a large single-copy (LSC) region of 85,784 bp and a small single-copy (SSC) region of 17,538 bp. The GC content of the chloroplast genome is 37.6%. There are 113 different genes in the chloroplast genome of B. kaoi, including 79 protein-coding genes, 30 tRNA genes, and four rRNA genes. A maximum-likelihood phylogenetic analysis showed that Bupleurum species is the monophyletic group, and B. kaoi belongs to subgenus Bupleurum and is closely related to B. scorzonerifolium.

SUBMITTER: Huang CC

PROVIDER: S-EPMC9415577 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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Complete chloroplast genome and phylogenetic analysis of Bupleurum kaoi Liu, Chao, and Chuang, 1977: an endemic species in Taiwan.

Huang Chi-Chun CC Huang Chao-Li CL Hsu Tsai-Wen TW Chang Li-Hui LH Hung Kuo-Hsiang KH Wang Wei-Kuang WK

Mitochondrial DNA. Part B, Resources 20220822 8

Bupleurum kaoi Liu, Chao, and Chuang is an endemic and endangered herb in Taiwan. In this study, the complete circular chloroplast genome of B. kaoi was reconstructed and annotated using Illumina sequencing. The genome size of B. kaoi is 155,938 bp, including a pair of inverted repeat regions (IRs: 26308 bp), separated by a large single-copy (LSC) region of 85,784 bp and a small single-copy (SSC) region of 17,538 bp. The GC content of the chloroplast genome is 37.6%. There a ...[more]

PMID: 36034531

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Project description:BackgroundAs 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.ResultsThe 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.ConclusionsThe 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.

Dataset Information

Complete chloroplast genome and phylogenetic analysis of Bupleurum kaoi Liu, Chao, and Chuang, 1977: an endemic species in Taiwan.

Publications

Complete chloroplast genome and phylogenetic analysis of <i>Bupleurum kaoi</i> Liu, Chao, and Chuang, 1977: an endemic species in Taiwan.

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