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植物研究 ›› 2016, Vol. 36 ›› Issue (5): 747-752.doi: 10.7525/j.issn.1673-5102.2016.05.016

• 研究报告 • 上一篇    下一篇

基于高通量测序分析青藏高原特有植物蓝玉簪龙胆(Gentiana veitchiorum)的SSR和SNP特征

田尊哲1,2, 高庆波1, 陈世龙1, 张发起1   

  1. 1. 中国科学院高原生物适应与进化重点实验室, 中国科学院西北高原生物研究所, 西宁 810001;
    2. 中国科学院大学, 北京 100039
  • 收稿日期:2016-03-31 出版日期:2016-09-15 发布日期:2016-09-27
  • 通讯作者: 张发起,E-mail:fqzhang@nwipb.cas.cn E-mail:fqzhang@nwipb.cas.cn
  • 作者简介:田尊哲(1989-),男,硕士研究生,主要从事植物遗传多样性学研究。
  • 基金资助:
    国家自然科学基金(31400322);青海省国际科技合作项目(2014-HZ-812)

Characteristics of SSR and SNP in Gentiana veitchiorum in Qinghai-Tibetan Plateau,by High-throughput Sequencing

TIAN Zun-Zhe1,2, GAO Qing-Bo1, CHEN Shi-Long1, ZHANG Fa-Qi1   

  1. 1. Key laboratory of Adaption and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810001;
    2. University of Chinese Academy of Sciences, Beijing 100039
  • Received:2016-03-31 Online:2016-09-15 Published:2016-09-27
  • Supported by:
    National Natural Science Foundation of China(31400322);International S&T cooperation projects of Qinghai Province(2014-HZ-812)

摘要: 利用Illumina HiSeqTM2500平台对青海省库泽县的蓝玉簪龙胆(Gentiana veitchiorum)进行高通量测序,共得到SSR序列8 588条,对其SSR重复类型进行分析;三核苷酸重复类型所占的比例最大占54.7%(4696);其次是二核苷酸重复类型占41.3%(3543);四核苷酸重复类型,五核苷酸重复类型和六核苷酸重复类型所占的比例较少(共占4%)。在二核苷酸重复类型中AT/TA重复类型所占的比例最大分别为9.85%和9.5%。在微卫星中重复单元的长度大小和重复次数成负相关,并且微卫星的总长度与重复单元的长度成正相关。在蓝玉簪龙胆的花(GP-F)和叶(GP-L)中分别得到253 789和249 417个SNP位点,其中在非编码区上的比例为51.29%和51.96%。分析发现蓝玉簪龙胆SNP位点在编码区中同义转换所占的比例(48.63%和47.96%)要远远高于非同义转换的比例(0.08%和0.08%),可能与功能基因序列相对稳定有关。

关键词: 蓝玉簪龙胆, 高通量测序, 微卫星, 单核苷酸多态性, 青藏高原

Abstract: We used the next generation sequencing(NGS) to capture the SSR and SNP marker in Gentiana veitchiorum, sampled in Zeku, Qinghai Province. A total of 8588 simple sequence repeats were generated through lumina HiSeqTM 2500. The dinucletide repeats were the highest(54.7%), followed by the trinucleotide repeats(41.3%). A proportion of tetranucletide, pentanucleotide and hexanucleotide repeats was less, which is 4% in total. In dinucleotide repeats, AT/TA repeats were the dominated ones, 9.85% and 9.5%, respectively. The length of nucleotide repeat and number of repeat were negative correlation, while there was a positive correlation between the total length of SSR sequences and the length of nucleotide repeat. A total of 253 789 and 249 417 SNPs were indenfied in GP-F and GP-L of G.veitchiorum. The proportion of the SNPs located in the noncoding region were 51.29% and 51.96%, respectively. The proportion of synonymous transition(48.63% and 47.96%) in coding region was significantly higher than that of nonsynonymous transition(0.08% and 0.08%), which might be caused by relatively conservative domains of functional genes.

Key words: Gentiana veitchiorum, next generation sequencing, SSR, SNP, Qinghai-Tibetan Plateau

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