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

doi:10.7525/j.issn.1673-5102.2016.05.016

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

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. 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-Zhe^1,2, GAO Qing-Bo¹, CHEN Shi-Long¹, ZHANG Fa-Qi¹

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/Abstract

摘要： 利用Illumina HiSeq^TM2500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 HiSeq^TM 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

中图分类号:

Q949.776.4

田尊哲, 高庆波, 陈世龙, 张发起. 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[J]. 植物研究, 2016, 36(5): 747-752.

TIAN Zun-Zhe, GAO Qing-Bo, CHEN Shi-Long, ZHANG Fa-Qi. Characteristics of SSR and SNP in Gentiana veitchiorum in Qinghai-Tibetan Plateau,by High-throughput Sequencing[J]. Bulletin of Botanical Research, 2016, 36(5): 747-752.

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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

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

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