利用高通量测序分析青藏高原地区青杨的SSR和SNP特征

雷淑芸; 张发起; Khan Gulzar; 王久利; 刘海瑞; 陈世龙

利用高通量测序分析青藏高原地区青杨的SSR和SNP特征

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, 青海西宁 810008
2.
中国科学院大学, 北京 100049
3.
西南大学生命科学学院, 重庆 400715
基金项目:
国家自然科学基金(31270270)、青海省国际科技合作项目(2014-HZ-812)
中图分类号: S718.46

Characteristic Analysis of SSR and SNP in Populus cathayana on the Qinghai-Tibetan Plateau by High-Throughput Sequencing

1.
Key laboratory of Adaption and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, Qinghai, China
2.
University of Chinese Academy of Sciences, Beijing 100039, China
3.
School of Life Sciences, Southwest University, Chongqing 400715, China
CLC number: S718.46

摘要: 利用Illumina HiSeqTM 2000平台对采自青海玉树的青杨进行高通量测序,SSR分析共获得7 067条SSR序列,复合型SSR共525条,发生频率0.149,平均跨度4 531.87 bp。SSR重复类型中,单核苷酸重复类型最多(33.96%);三核苷酸重复类型次之(31.00%);二核苷酸重复类型位居第三(27.69%);四核苷酸、五核苷酸、六核苷酸重复类型SSR含量很少(<8%)。二核苷酸重复类型中,AG重复类型所占比例最高,GA次之,CT、TC则紧随其后;三核苷酸重复类型中,AAG重复类型所占比例最高,GAA次之,TTC、AGA、GAG、CAG、TCT、TGG等重复类型数量相近。SNP分析发现,L1A中含SNP 162 343个,L2A中含SNP 229 115个。SNP 类型中,转换类型明显高于颠换类型,L1A中转换类型占61.06%,颠换类型占38.94%,L2A中转换类型占61.27%,颠换类型占38.73%。转换类型中,C-T发生频率最高,分别为30.75%、30.66%,A-G发生频率与C-T相差不大,分别为30.31%、30.62%。L1A和L2A 中SNPs类型及其发生频率变化趋势基本一致,L2A中与L1A中相对应的同一SNPs类型的数量之比约为2∶ 1。分析表明,在青杨的遗传多样性中,SNP标记较SSR标记更为可靠。
- 青杨
- / 青藏高原
- / 高通量测序
- / 微卫星
- / 单核苷酸多态性
Abstract: Two samples of Populus cathayana from Yushu were sequenced with high-throughput sequencing technology (Illumina HiSeqTM 2000). A total of 7076 sequences were hunted for microsatellites analysis, including 525 compound microsatellite sequences. The results showed that the mononucleotide repeats were the highest (33.96%), followed by trinucleotide repeats (31.00%) and dinucleotide repeats 27.69%. The tetranucleotide, pentanucleotide and hexanucleotide repeats were all less than 8%. Among the dinnucleotide repeats, the AG repeats were with highest frequency followed by GA, CT and TC respectively. Similarly in trinucleotide repeats, the AAG repeats were the highest followed by GAA, TTC, AGA, GAG, CAG, TCT and TGG. In the single nucleotide polymorphism, the transition types were higher than transversion in both samples. In sample L1A, the transition types of SNPs were 61.06% while the transversion types were 38.94%. In sample L2A, the transition types were 61.27%, while the transversion types were 38.73%. Among the transitions of two samples, C-T occurrences frequencies were the most, 30.75% and 30.66% respectively. A-G occurrences frequencies were similar to C-T, list to the second (30.31% and 30.62%). In both samples, the single nucleotide polymorphism trends were similar. The ratios of the same single nucleotide polymorphism in both samples were 2∶ 1. The results of analysis indicated that the SNP was a more reliable maker in geneticdiversity than SSR.
- Populus cathayana
- / Qinghai-Tibetan Plateau
- / high-throughput sequencing
- / SSR
- / SNP

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利用高通量测序分析青藏高原地区青杨的SSR和SNP特征

Characteristic Analysis of SSR and SNP in Populus cathayana on the Qinghai-Tibetan Plateau by High-Throughput Sequencing

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利用高通量测序分析青藏高原地区青杨的SSR和SNP特征

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Characteristic Analysis of SSR and SNP in Populus cathayana on the Qinghai-Tibetan Plateau by High-Throughput Sequencing

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利用高通量测序分析青藏高原地区青杨的SSR和SNP特征

Characteristic Analysis of SSR and SNP in Populus cathayana on the Qinghai-Tibetan Plateau by High-Throughput Sequencing

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利用高通量测序分析青藏高原地区青杨的SSR和SNP特征

English Abstract

Characteristic Analysis of SSR and SNP in Populus cathayana on the Qinghai-Tibetan Plateau by High-Throughput Sequencing

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目录