鲚属单核苷酸多态性位点(SNPs)标记开发及在物种界定中的应用初探

单核苷酸多态性(SNP)分子标记结合二代测序技术是研究群体遗传学强有力的工具,同时也是界定物种的最佳方法之一。与以往获取SNPs数据的常用方法相比,靶基因富集的方法可以用来富集不同物种的同源片段,甚至可以用于部分降解的DNA。本研究应用一套通用的脊椎动物单拷贝核基因标记,通过基因富集和Illumina测序获取鲱形目鲚属数千个SNPs位点。样本取自靠近长江入海口的沿海地区、长江干流和洞庭湖。用STRUCTURE和Bayes factor delimitation(*with genomic data,BFD*:一种新的物种界定工具)分析SNPs数据,发现洞庭湖的短颌鲚显著不同于其他采样点的样本,而从沿海地区采集的刀鲚与长江干流的个体之间的差异不明显(Bayes factor=11.3)。研究表明,基因富集可以用来获得非模式生物的SNPs数据,结合新的分析工具如BFD*可用于物种界定。

Developing SNP markers for Coilia and its application in species delimitation

Single nucleotide polymorphism (SNP) markers coupled with the next-generation sequencing technologies are powerful tools for studying population genetics, as well as for species delimitation. The popular ways of obtaining SNP data include RNA sequencing and restriction site associated DNA (RAD) sequencing. However, both methods have limitations. For example, RNA sequencing requires fresh tissue samples, whereas RAD sequencing targets anonymous loci usually not transferable across species. In comparison with these methods, target gene capture could be used to enrich homologous fragments across divergent species and even from degraded DNA. We showed that by targeting a set of universal single-copy nuclear gene markers of vertebrates, we could retrieve thousands of SNPs from the Japanese grenadier anchovy (Coilia nasus) sampled from three locations: coastal region close to the estuary of the Yangtze River, the main stem of the river and Lake Dongting, a lake connected to the middle reach of the Yangtze River. We analyzed hundreds of representative SNPs from the data using STRUCTURE and Bayes factor delimitation (*with genomic data; BFD*), a new Bayesian species delimitation tool. We found that the fish from Lake Dongting are genetically different from the fish of rest sample locations. We also observed marginal difference between fish collected from the coastal region and the main stem of the Yangtze River (Bayes factor = 11.3). Our study demonstrated that gene capture could be used to generate SNP data for species delimitation applying new analytic tools such as BFD*.