基于蛇足石杉转录组的SNP和SSR多态性分析

Mining and Analyzing SNP and SSR Molecular Markers based on Transcriptome Sequences of Huperzia serrata

目的:对蛇足石杉的单核苷酸多态性(SNP)及微卫星短序列重复多态性(SSR)进行分析。方法:用HISAT、GATK、MISA等软件对蛇足石杉转录组筛选得到SNP和SSR并设计了SSR引物。结果:共发现50 388个SNP位点,转换占64. 2%,颠换占35. 8%。共筛选出11 934条SSR,分布在9 358个unigene中,其中含有两条以上SSR的unigene有1 786个。二核苷酸重复出现频率最多,占总SSR47. 6%,三核苷酸重复占31. 2%,六核苷酸重复占10%、单核苷酸重复占4. 2%、四核苷酸重复占3. 9%,最少的是五核苷酸重复占3. 1%。结论:蛇足石杉具有较丰富的SNP和SSR标记,为其品种鉴定、种质培育等研究奠定了基础。

Objective:To analyze the single nucleotide polymorphism (SNP) and microsatellite short sequence polymorphism (SSR) of Huperzia serrata. Methods:SNP and SSR were screened by HISAT, GATK, MISA and other software for S. serrata transcriptome and SSR primers were designed. Results:A total of 50 388 SNP loci were found, with conversion accounting for 64.2% and transversion accounting for 35.8%.A total of 11 934 SSRs were screened and distributed in 9 358 unigenes, of which 1 786 were unigenes containing more than two SSRs. Dinucleotide repeats occur most frequently, accounting for 47.6% of total SSR, 31.2% of trinucleotide repeats, 10% of hexanucleotide repeats, 4.2% of single nucleotide repeats, and 3.9 % of tetranucleotide repeats. The least repeat is a five nucleotide repeat of 3.1%. Conclusion:Scylla serrata has abundant SNP and SSR markers, which lays a foundation for its cultivar identification and germplasm cultivation.