藏波罗花叶绿体基因组分析

Analysis of the chloroplast genome of Incarvillea younghusbandii Sprague

摘要:

藏波罗花（Incarvillea younghusbandii Sprague）是一种传统的补益类中药。其根作草药使用，用于滋补强壮，治产后少乳、久病虚弱、头晕、贫血等症。但目前关于藏波罗花分子遗传信息的研究很少。本研究基于高通量测序技术对藏波罗花叶绿体基因组进行测序、组装和注释，并对其序列特征、密码子偏好性、重复序列、系统发育和分化时间进行分析。结果表明，藏波罗花叶绿体基因组全长为159 323 bp，包含1个大单拷贝区（80 197 bp）、1个小单拷贝区（9 030 bp）和2个反向重复区（35 048 bp）；共注释出120个基因，包括77个蛋白编码基因、8个rRNA基因和35个tRNA基因；密码子偏好性分析显示，AAA是藏波罗花叶绿体基因组中使用最频繁的密码子；从藏波罗花叶绿体基因组中共检测到42个简单重复序列（simple sequence repeats，SSR）；系统发育分析表明，藏波罗花与密生波罗花（Incarvillea compacta）的亲缘关系最近，且在大概466万年前产生分化。本研究对藏波罗花相关资源的科学保护和开发具有重要的现实意义，也可以为后续角蒿属（Incarvillea）的物种鉴定、紫葳科（Bignoniaceae）的种群遗传多样性研究提供基本的遗传资源。

关键词:藏波罗花;叶绿体基因组;密码子偏好性;简单重复序列;系统发育分析;分化时间估计

Abstract:

Incarvillea younghusbandii Sprague is a traditional tonic herb. The roots are used as herbal medicine for nourishing and strengthening, as well as treating postpartum milk deficiency and weakness. In this study, the chloroplast genome of I. younghusbandii was sequenced and assembled by the high-throughput sequencing technology. The sequence characteristics, sequence repeats, codon usage bias, phylogenetic relationships and estimated divergence time of I. younghusbandii were analyzed. The 159 323 bp sequence contained a large single copy (80 197 bp), a small single copy (9 030 bp) and two inverted repeat sequences (35 048 bp). It contained 120 genes, including 77 protein coding genes, 8 ribosomal RNA genes and 35 transfer RNA genes. AAA was the most frequent codon in the chloroplast coding sequence of I. younghusbandii. A total of 42 simple sequence repeats were identified in the chloroplast genome. Phylogenetic analysis revealed I. younghusbandii was mostly like its taxonomically close relative Incarvillea compacta. The divergence between I. younghusbandii and I. compacta was dated to 4.66 million years ago. This study was significant for the scientific conservation and development of resources related to I. compacta. It also provides a basic genetic resource for the subsequent species identification of the genus Incarvillea, and the population genetic diversity study of Bignoniaceae.

Key words:Incarvillea younghusbandii;complete chloroplast genome;codon usage bias;simple sequence repeats (SSR);phylogenetic;estimated divergence time