比较分析南蛇藤属（卫矛科）物种的叶绿体基因组：为分子进化、物种鉴定和系统发育关系提供见解。

Comparative analysis the chloroplast genomes of Celastrus (Celastraceae) species: Provide insights into molecular evolution, species identification and phylogenetic relationships.

机构信息

School of Life Sciences and Biopharmaceutics, Guangdong Provincial Key Laboratory of Pharmaceutical Bioactive Substances, Guangdong Pharmaceutical University, Guangzhou, 510006, China.

School of Pharmacy, Guangdong Pharmaceutical University, Guangzhou 510006, China.

出版信息

Phytomedicine. 2024 Aug;131:155770. doi: 10.1016/j.phymed.2024.155770. Epub 2024 May 29.

DOI:10.1016/j.phymed.2024.155770

PMID:38851103

Abstract

BACKGROUND

The genus Celastrus is an important medicinal plant resource. The similarity of morphology and the lack of complete chloroplast genome analysis have significantly impeded the exploration of species identification, molecular evolution and phylogeny of Celastrus.

PURPOSE

In order to resolve the phylogenic controversy of Celastrus species, the chloroplast genome comparative analysis was performed to provide genetic evidence.

METHODS

In this study, we collected and sequenced ten chloroplast genomes of Celastrus species from China and downloaded three chloroplast genomes from the databases. The chloroplast genomes were compared and analyzed to explore their characteristics and evolution. Furthermore, the phylogenetic relationships of Celastrus species were inferred based on the whole chloroplast genomes and protein-coding genes.

RESULTS

All the 13 Celastrus species chloroplast genomes showed a typical quadripartite structure with genome sizes ranging from 155,113 to 157,366 bp. The intron loss of the rps16 gene occurred in all the 13 Celastrus species. The GC content, gene sequence, repeat types and codon bias pattern were highly conserved. Ten highly variation regions were identified, which can be used as potential DNA markers in molecular identification of Celastrus species. Eight genes, including accD, atp4, ndhB, rpoC1, rbcL, rpl2, rpl20 and ycf1, were detected to experience positive selection. Phylogenetic analysis showed that Celastrus was a monophyletic group and Tripterygium was the closest sister-group. Noteworthy, C. gemmatus Loes. and C. orbiculatus Thunb. can be discriminated using the chloroplast genome as a super barcode. The comparative and phylogenetic analysis results proposed that C. tonkinensis Pitard. was the synonym of C. hindsii Benth.

CONCLUSION

The comparative analysis of the Celastrus chloroplast genomes can provide comprehensive genetic evidence for molecular evolution, species identification and phylogenetic relationships.

摘要

背景

南蛇藤属是一种重要的药用植物资源。由于形态相似和缺乏完整的叶绿体基因组分析，严重阻碍了南蛇藤属物种鉴定、分子进化和系统发育的研究。

目的

为了解决南蛇藤属物种的系统发育争议，进行叶绿体基因组比较分析，提供遗传证据。

方法

本研究从中国收集并测序了 10 种南蛇藤属植物的叶绿体基因组，并从数据库中下载了 3 种叶绿体基因组。对叶绿体基因组进行比较和分析，以探讨其特征和进化。此外，基于叶绿体全基因组和蛋白编码基因推断了南蛇藤属物种的系统发育关系。

结果

所有 13 种南蛇藤属植物的叶绿体基因组均表现出典型的四分体结构，基因组大小在 155113 到 157366bp 之间。所有 13 种南蛇藤属植物的 rps16 基因均发生了内含子缺失。GC 含量、基因序列、重复类型和密码子偏好模式高度保守。鉴定出 10 个高度变异区，可作为南蛇藤属植物分子鉴定的潜在 DNA 标记。发现 8 个基因（accD、atp4、ndhB、rpoC1、rbcL、rpl2、rpl20 和 ycf1）经历了正选择。系统发育分析表明，南蛇藤属是一个单系群，雷公藤是最接近的姐妹群。值得注意的是，叶绿体基因组可作为南蛇藤属植物的超级条形码，将其分为两个种，即南蛇藤（Celastrus gemmatus Loes.）和南蛇藤（Celastrus orbiculatus Thunb.）。比较和系统发育分析结果表明，山蒟藤（C. tonkinensis Pitard.）是黑老虎（C. hindsii Benth.）的同物异名。