西南牡蒿叶绿体基因组特征及系统发育分析

Chloroplast genome features and phylogenetic analysis of Artemisia parviflora

关键词:  西南牡蒿, 叶绿体基因组, 密码子使用偏性, 分子标记, 系统发育分析

Key words:  Artemisia parviflora, chloroplast genome, codon usage bias, molecular markers, phylogenetic analysis

摘要:

为探究西南牡蒿(Artemisia parviflora)的叶绿体基因组结构特征及其系统位置,该研究利用高通量测序技术对其进行测序,并借助生物信息学工具进行分析。结果表明:(1)西南牡蒿叶绿体基因组长151 047 bp,呈现为由4部分组成的环状双链结构,GC含量为37.5%。(2)共注释115个基因,包括81个蛋白编码基因、4个rRNA基因及30个tRNA基因。(3)检测到68个简单重复序列(SSRs)和37个长重复序列。(4)西南牡蒿叶绿体基因组的密码子使用偏性较弱,其主要受自然选择的影响,高频密码子偏向以A/U结尾。(5)西南牡蒿叶绿体基因组的IR区未出现明显的扩张或收缩; 筛选出了trnH-psbA、rpl16-rps3、ycf15-trnL-UAG、ndhA和ycf1 5个高变异区域,可作为鉴定龙蒿亚属植物的潜在分子标记。(6)系统发育分析揭示了西南牡蒿在龙蒿亚属中的系统位置及蒿属内各亚属的系统发育关系。该研究为蒿属植物后续的分子标记开发和系统发育研究提供了参考。

Abstract:

To explore the structural features of Artemisia parviflora chloroplast genome and its systematic position, high-throughput sequencing technology were employed for genome sequencing and bioinformatics tools for analyzing. The results were as follows:(1)The chloroplast genome of A. parviflora was 151 047 bp, with a typical circular double-stranded tetrad structure, and the GC content was 37.5%.(2)Total 115 unique genes were annotated, including 81 protein-coding genes, 4 rRNA genes, and 30 tRNA genes.(3)Sixty-eight simple sequence repeats(SSRs)and 37 long repeat sequences were detected.(4)The codon usage bias was weak in the A. parviflora chloroplast genome, and natural selection mainly contributed to the codon usage bias. High-frequency codons tend to ended with A/U.(5)There was no obvious expansion or contraction of the inverted repeat(IR)regions. Five high variation regions(trnH-psbA, rpl16-rps3, ycf15-trnL-UAG, ndhA, and ycf1)were identified which could be used as potential molecular markers for identifying subgen. Dracunculus species.(6)Phylogenetic analysis revealed the systematic position of A. parviflora within subgen. Dracunculus and elucidated the phylogenetic relationships among the various subgenera of Artemisia. This study provides the reference for future molecular marker development and phylogenetic research of Artemisia species.