西藏 13 种唇形科植物叶绿体基因组结构及系统发育分析。

Chloroplast Genome Structure and Phylogenetic Analysis of 13 Lamiaceae Plants in Tibet.

机构信息

The Research Center for Traditional Chinese Medicine Resources and Ethnic Minority Medicine, Jiangxi University of Chinese Medicine, 330004 Nanchang, Jiangxi, China.

出版信息

Front Biosci (Landmark Ed). 2023 Jun 8;28(6):110. doi: 10.31083/j.fbl2806110.

DOI:10.31083/j.fbl2806110

PMID:37395020

Abstract

BACKGROUND

The chloroplast (cp) genome has unique and highly conserved characteristics and is therefore widely used in species identification and classification, as well as to improve the in-depth understanding of plant evolution.

METHODS

In this study, the cp genomes of 13 Lamiaceae plants in the Tibet Autonomous Region of China were sequenced, assembled and annotated using bioinformatics methods. Phylogenetic trees were constructed to reveal the phylogenetic relationship of related species in the Lamiaceae.

RESULTS

The results showed that all 13 cp genomes had a typical four-segment structure, including one large single-copy (LSC) region, one pair of inverted repeat (IR) regions and one small single-copy (SSC) region. The sequence lengths of the 13 cp genomes were between 149,081 bp and 152,312 bp, and the average GC content was 37.6%. These genomes contained 131-133 annotated genes, including 86-88 protein-coding genes, 37-38 tRNA genes, and 8 rRNA genes. A total of 542 SSR loci were detected using MISA software. The repeat types were mostly single-nucleotide repeats, accounting for 61% of simple repeats. A total of 26,328-26,887 codons were detected in 13 cp genomes. According to the RSCU value analysis, the codons mostly ended with A/T. Analysis of IR boundaries showed that the other species were relatively conserved, except for (D. Don) Hand.-Mazz., which differed in gene type and location on both sides of the boundary. By analysing nucleotide diversity, two highly mutated regions located in the LSC and SSC regions were identified in the 13 cp genomes.

CONCLUSIONS

Using the cp genome of Murray as the outgroup, 97 cp genomes of the Lamiaceae were used to construct an Maximum Likehood (ML) phylogenetic tree, in which these species were divided into eight major clades, corresponding to eight subfamilies based on morphological classification. The phylogenetic results based on monophyletic relationships were consistent with the morphological classification status at the tribe level.

摘要

背景

叶绿体（cp）基因组具有独特且高度保守的特征，因此被广泛用于物种鉴定和分类，以及深入了解植物进化。

方法

本研究采用生物信息学方法对中国西藏自治区 13 种唇形科植物的 cp 基因组进行测序、组装和注释。构建系统发育树以揭示唇形科相关物种的系统发育关系。

结果

结果表明，所有 13 个 cp 基因组均具有典型的四段结构，包括一个大单拷贝（LSC）区、一对反向重复（IR）区和一个小单拷贝（SSC）区。13 个 cp 基因组的序列长度在 149081bp 到 152312bp 之间，平均 GC 含量为 37.6%。这些基因组包含 131-133 个注释基因，包括 86-88 个蛋白编码基因、37-38 个 tRNA 基因和 8 个 rRNA 基因。使用 MISA 软件共检测到 542 个 SSR 位点。重复类型主要为单核苷酸重复，占简单重复的 61%。在 13 个 cp 基因组中共检测到 26328-26887 个密码子。根据 RSCU 值分析，密码子大多以 A/T 结尾。IR 边界分析表明，除（D. Don） Hand.-Mazz. 外，其他物种相对保守，该物种在边界两侧的基因类型和位置均有差异。通过分析核苷酸多样性，在 13 个 cp 基因组中鉴定出两个位于 LSC 和 SSC 区域的高度突变区域。