Targeted re-sequencing of coding DNA sequences for SNP discovery in non-model species

Targeted capture coupled with high throughput sequencing can be used to gain information about nuclear sequence variation at hundreds to thousands of loci. Divergent reference capture makes use of molecular data of one species to enrich target loci in other (related) species. This is particularly valuable for non-model organisms, for which often no a priori knowledge exists regarding these loci. Here, we have used targeted capture to obtain data for 809 nuclear coding DNA sequences (CDS) in a non-model organism, the Eurasian lynx Lynx lynx, using baits designed with the help of the published genome of a related model organism (the domestic cat Felis catus). Using this approach, we were able to survey intraspecific variation at hundreds of nuclear loci in L. lynx across the species’ European range. A large set of bi-allelic candidate SNPs was then evaluated using a high throughput SNP-genotyping platform (Fluidigm), which we then reduced to a final 96 SNP-panel based on assay performance...靶向捕获（targeted capture）结合高通量测序（high throughput sequencing）技术，可用于获取数百至数千个基因座（loci）的核序列变异信息。歧化参考捕获（Divergent reference capture）利用单一物种的分子数据，对其他（亲缘）物种的靶标基因座进行富集。该技术对于非模式生物（non-model organisms）尤为实用，因为这类生物通常缺乏相关基因座的先验知识（a priori knowledge）。本研究借助亲缘模式生物家猫（*Felis catus*）已发表的基因组设计捕获探针，对非模式生物欧亚猞猁（*Lynx lynx*）的809个核编码DNA序列（CDS）开展靶向捕获并获取测序数据。通过该方法，本研究对分布于欧洲全境的欧亚猞猁种群的数百个核基因座完成了种内变异（intraspecific variation）调查。随后，研究人员利用高通量SNP基因分型平台（Fluidigm）对大量双等位基因候选单核苷酸多态性（SNPs）进行筛选，并基于分型实验表现，最终得到包含96个位点的SNP分型面板。