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

doi:10.7525/j.issn.1673-5102.2016.05.016

Abstract

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

CLC Number:

Q949.776.4

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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