东海带鱼(Trichiurus japanicus)肝脏转录组SSR和SNP特征分析

SSR and SNP analysis based on Trichiurus japanicus transcriptome

本研究以东海带鱼转录组测序数据为基础,采用MISA软件进行SSR筛选,利用Samtools和GATK进行SNP筛选,并进行SSR和SNP的特征分析。结果共获得SSR49311个,其中完整的微卫星共有44625个,复合型SSR数目为4687个。SSR片段长度11~374bp。重复长度小于20bp的序列,有30997条,其中长度在12~20bp的SSR为7523个,约占总数的29.35%,呈中等多态性,重复长度大于20bp长序列为13627个,约占总数的53.18%,呈较高多态性;共获得SNP位点数876199个,其中颠换335218个,转换540981个,转换、颠换比例为1.61∶1。在非编码区的SNP数量为578020个;在编码区的SNP总数298179个,在编码区的碱基转换类型中C→T占比最高,为22.09%。另本研究提供了SSR和SNP原始引物各10对。研究结果可为今后带鱼的分子标记开发、遗传连锁图谱构建以及种质资源保护等提供基础数据。

SSR and SNP of Trichiurus japanicus were screened and analyzed respectively by MISA software,Samtools and GATK,basing on the transcriptome sequencing data of Trichiurus japanicus .Results showed the total number of SSRs were 49 311,including 44 625 complete microsatellites.The number of composite SSRs were 4 687.The size of SSR segment ranged from 11 to 374.There were 30 997 sequences with repetition length less than 20 bp.Among them,there were 7 523 SSRs with length between 12 and 20 bp,accounting for about 29.35% of the total number,showing medium polymorphism.And 13 627 long sequences with repetition length greater than 20 bp,accounting for about 53.18% of the total number,showing high polymorphism.A total of 876 199 SNP bits were obtained,including 335 218 transversals,540 981 transversals,and the ratio of transversals to transversals was 1.61∶ 1.The number of SNPs in the non-coding region was 578 020.There were a total of 298 179 SNPs in the coding area.Among the base conversion types in the coding area,“C” to “T” accounted for the highest proportion,which was 22.09%.In addition,10 pairs of original primers of SSR and SNP were respectively provided in this study.This study could provide important scientific basis for the development of molecular markers,the construction of genetic linkage map and the protection of germplasm resources in the future.