基于SLAF测序分析3个塔形马蹄螺群体的遗传结构和多样性

Genetic Structure and Diversity Analysis of Three Natural Populations of Tectus pyramis Based on Specific Locus Amplified Fragment Sequencing

塔形马蹄螺(Tectus pyramis),海洋软体动物,广泛分布于中国深圳大鹏湾、海南岛、西沙和南沙群岛的珊瑚礁生态系统中。文章采用特异性位点扩增片段简化基因组测序技术(SLAF-seq)对来自深圳(SZ)、三亚(SY)和西沙(XS)的塔形马蹄螺群体的遗传多样性和结构进行分析。通过测序共获得115.74Mb读长数据,平均测序深度为337.87倍,测序质量值(Q30)平均为94.07%。研究获得118679个多态性SLAF标签,获得846502个高度一致的群体单核苷酸多态性位点(SNPs),其中有155个显著差异SNPs。3个群体的平均观察杂合度(Ho)和期望杂合度(He)值分别为0.1441~0.1611和0.2537~0.2695。平均多态性信息含量(PIC)为0.2048~0.2176。通过系统发育树分析、主成分分析和聚类分析,将45个个体大致分为3个类群,每个群体的所有个体都可以聚类成一个类群。SZ和SY群体的遗传结构相似,遗传距离最低(0.2510),遗传分化系数Fst值最低(0.0818)。但XS与其他两个群体间的遗传分化明显,尤其是XS和SZ群体(Fst=0.1868)。3个群体的遗传分化可能与海流和地理位置有关。

The marine mollusc Tectus pyramis inhabits the coral reef ecosystems surrounding Dapeng Bay in Shenzhen(SZ),Hainan Island,Xisha(XS)and Nansha Islands of China.In this study,the genetic diversity and genetic structure of three natural populations of T.pyramis from SZ,Sanya(SY)and XS were assessed using specific locus amplified fragment(SLAF)sequencing.A total of 115.74 Mb reads was obtained,with an average depth of 337.87-fold,and an average Q30 value of 94.07%.Based on 118679 polymorphic SLAF tags,we obtained 846502 highly consistent population single-nucleotide polymorphisms(SNPs),and found 155 SNPs displayed significant differences between populations.Average observed(Ho)and expected(He)heterozygosity values for the three populations ranged from 0.1441 to 0.1611 and from 0.2537 to 0.2695,respectively.Average polymorphism information content(PIC)values were between 0.2048 and 0.2176.The 45 individuals were roughly divided into three groups by phylogenetic tree analysis,principal component analysis(PCA)and clustering;and all the individuals from each population could be clustered into a single group.The genetic structures of SZ and SY populations were similar,yielding the lowest genetic distance(0.2510)and Fst value(0.0818).However,genetic differentiation between XS and the other two populations was significant,especially between SX and SZ(Fst=0.1868).Genetic differentiation of the three populations may be correlated to ocean currents and geographical locations.The results of this study provide a theoretical basis for germplasm resource management and future aquaculture breeding programs.