生物多样性 ›› 2019, Vol. 27 ›› Issue (4): 366-372.DOI: 10.17520/biods.2018332

• 研究报告: 植物多样性 • 上一篇    下一篇

直刺变豆菜叶绿体全基因组及其特征

陈志祥1,姚雪莹1,Stephen R.Downie2,王奇志1,*()   

  1. 1 华侨大学化工学院园艺系, 福建厦门 361021
    2 Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana 61801
  • 收稿日期:2018-12-18 接受日期:2019-01-09 出版日期:2019-04-20 发布日期:2019-06-05
  • 通讯作者: 王奇志
  • 基金资助:
    国家自然科学基金(31500162);国家标本平台教学标本子平台项目(2005DKA21403-JK);华侨大学研究生科研创新能力培育计划资助项目(1611315007);中国大学校园植物网的构建与示范Ⅱ(20180947)

Assembling and analysis of Sanicula orthacantha chloroplast genome

Chen Zhixiang1,Yao Xueying1,Stephen R. Downie2,Wang Qizhi1,*()   

  1. 1 Department of Horticulture, Huaqiao University, Xiamen, Fujian 361021, China
    2 Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana 61801
  • Received:2018-12-18 Accepted:2019-01-09 Online:2019-04-20 Published:2019-06-05
  • Contact: Wang Qizhi

摘要:

直刺变豆菜(Sanicula orthacantha)是中国广泛分布的多年生草本植物, 也是一味著名的民族药。本文通过二代高通量测序平台Illumina HiSeq PE150对直刺变豆菜叶绿体全基因组进行测序, 并通过生物信息学方法对其结构特征进行分析。结果表明: 直刺变豆菜叶绿体全基因组大小为157,163 bp, 包括大单拷贝区(large single copy, LSC)、小单拷贝区(small single copy, SSC)和2个反向重复序列(inverted repeat sequence, IRa和IRb), 长度分别为87,547 bp、17,122 bp和26,247 bp, 具有典型被子植物叶绿体基因组环状四分体结构; 共注释得到129个基因, 包括8个核糖体RNA (rRNA)基因、37个转运RNA (tRNA)基因和84个蛋白质编码基因。直刺变豆菜在叶绿体基因组结构、基因种类、排列顺序上与其他伞形科植物基本一致。直刺变豆菜叶绿体全基因组测序的成功为变豆菜属植物完整叶绿体基因组组装及其特征分析提供了新的方法。

关键词: 高通量测序, 变豆菜属, 基因组装, 系统发育分析

Abstract:

Sanicula orthacantha is a perennial herb widely distributed in China and is a widely used for medicinal purposes. In this study, the whole chloroplast genome was sequenced and analyzed using bioinformatics methods. The results showed that it was a circular molecule 157,163 bp in length with a typical quadripartite structure including a pair of inverted repeats (IRa and IRb) of 26,247 bp that were separated by large and small single copy regions (LSC and SSC) of 87,547 bp and 17,122 bp, respectively. A total of 129 predicted genes, including 84 protein-coding genes, 37 tRNA genes and eight rRNA genes were identified. Compared with other Apiaeceae species, the S. orthacantha chloroplast genome had few differences in size, order and structure. The success of sequencing the S. orthacantha chloroplast genome provides a new method for the complete chloroplast genome assembly and characterization of Sanicula species, providing a methodological guide for the study of Sanicula plant evolution and phylogeny.

Key words: high-throughput sequencing, Sanicula L., gene assembly, phylogenetic analysis