基于转录组测序的中华鳖SSR和SNP特征分析及性别标记筛选

Analysis of SSR and SNP Characteristics and Screening of Sex-linked Markers in Chinese Soft-shelled Turtle Based on Transcriptome Sequencing

【目的】挖掘更多中华鳖(Pelodiscus sinensis)性别分子标记,为中华鳖保护、繁育以及遗传多样性的分子机制等研究提供基础。【方法】基于中华鳖转录组测序数据,利用MISA和GATK挖掘中华鳖转录本中SSR和SNP位点信息,开发与中华鳖性别紧密相关的SNP标记。【结果和结论】共组装获得341632条Unigenes,识别到14804个SSR位点,含有SSR位点的Unigenes序列数量为13904条,占总序列的4.1%。中华鳖转录组中SSR位点类型较为丰富,共识别到6种不同核苷酸重复类型,单核苷酸串联重复基元类型的含量最多(10981个),占总位点数的74.18%。SSR位点以重复11~15次为主(6173个),占总位点数的41.70%。转录组SSR的片段长度大部分集中在10~14 bp,占SSR总数的50.01%。搜索到32299个SNP位点,SNP的分布密度为1/1339 bp。SNP变异类型以转换类型为主,转换类型占70.05%,颠换类型占29.95%。SNP测序深度统计发现,在31~100范围内,SNP数目最多,占43.68%。初步筛选并鉴定出位于Ptpn11基因上与性别紧密关联的SNP位点(29144910),为中华鳖性别分子标记提供候选基因和标记。

【Objective】To provide a scientific basis for the conservation,breeding,and molecular mechanism of genetic diversity of Pelodiscus sinecnsis by developing more sex-linked molecular markers.【Method】The SSR and SNP loci information in P.sinensis transcripts were mined by RAN Seq,MISA and GATK means.【Result and Conclusion】A total of 341632 Unigenes were obtained by splicing and assembly,and 14804 SSR loci were identified.The number of Unigenes sequences containing SSR loci was 13904,accounting for 4.1%of the total sequences.A total of six different nucleotide repeat types were identified in the SSR loci of P.sinensis transcriptome.Among them,the single nucleotide tandem repeat unit type was the most abundant(10981),accounting for 74.18%of the total number of loci.The SSR loci were mainly in the range of 11 to 15 repetitions(6173),accounting for 41.70%of the total number of loci.The fragment lengths of SSRs were mostly in the range of 10-14 bp,accounting for 50.01%of the total number of SSRs.A total of 32299 SNP loci were searched,with a distribution density of 1/1339 bp.The SNP variant type was mainly the conversion type,accounting for 70.05%,while the reversal type accounted for 29.95%.The SNP sequencing depth was mainly within the range of 31-100,accounting for 43.68%.In addition,29144910 SNP loci on Ptpn11 closely associated with sex,were further screened out and identified to provide candidate genes and markers for sex molecular markers in P.sinensis.