Data_Sheet_1_A New Single Nucleotide Polymorphism Database for Rainbow Trout Generated Through Whole Genome Resequencing.XLSX

Single-nucleotide polymorphisms (SNPs) are highly abundant markers, which are broadly distributed in animal genomes. For rainbow trout (Oncorhynchus mykiss), SNP discovery has been previously done through sequencing of restriction-site associated DNA (RAD) libraries, reduced representation libraries (RRL) and RNA sequencing. Recently we have performed high coverage whole genome resequencing with 61 unrelated samples, representing a wide range of rainbow trout and steelhead populations, with 49 new samples added to 12 aquaculture samples from AquaGen (Norway) that we previously used for SNP discovery. Of the 49 new samples, 11 were double-haploid lines from Washington State University (WSU) and 38 represented wild and hatchery populations from a wide range of geographic distribution and with divergent migratory phenotypes. We then mapped the sequences to the new rainbow trout reference genome assembly (GCA_002163495.1) which is based on the Swanson YY doubled haploid line. Variant calling was conducted with FreeBayes and SAMtools mpileup, followed by filtering of SNPs based on quality score, sequence complexity, read depth on the locus, and number of genotyped samples. Results from the two variant calling programs were compared and genotypes of the double haploid samples were used for detecting and filtering putative paralogous sequence variants (PSVs) and multi-sequence variants (MSVs). Overall, 30,302,087 SNPs were identified on the rainbow trout genome 29 chromosomes and 1,139,018 on unplaced scaffolds, with 4,042,723 SNPs having high minor allele frequency (MAF > 0.25). The average SNP density on the chromosomes was one SNP per 64 bp, or 15.6 SNPs per 1 kb. Results from the phylogenetic analysis that we conducted indicate that the SNP markers contain enough population-specific polymorphisms for recovering population relationships despite the small sample size used. Intra-Population polymorphism assessment revealed high level of polymorphism and heterozygosity within each population. We also provide functional annotation based on the genome position of each SNP and evaluate the use of clonal lines for filtering of PSVs and MSVs. These SNPs form a new database, which provides an important resource for a new high density SNP array design and for other SNP genotyping platforms used for genetic and genomics studies of this iconic salmonid fish species.

单核苷酸多态性（SNPs）是高度丰富的标记，广泛分布于动物基因组中。对于彩虹鳟（Oncorhynchus mykiss）而言，SNPs的发现先前是通过限制性位点关联DNA（RAD）文库、缩减代表性文库（RRL）和RNA测序实现的。近期，我们对61个无关联样本进行了高覆盖全基因组重测序，这些样本代表了广泛的彩虹鳟和钢头鳟种群，其中新增了49个样本，与之前用于SNPs发现的来自挪威AquaGen（Aquagen）的12个养殖样本相结合。在这49个新样本中，有11个来自华盛顿州立大学（WSU）的双倍体纯合系，其余38个代表了广泛地理分布和具有不同迁徙表型的野生和养殖种群。随后，我们将序列映射到新的彩虹鳟参考基因组组装（GCA_002163495.1），该组装基于Swanson YY双倍体纯合系。变异调用是通过FreeBayes和SAMtools mpileup进行的，随后根据质量分数、序列复杂度、位点的读深以及基因型样本的数量对SNPs进行筛选。将两种变异调用程序的结果进行比较，并使用双倍体纯合样本的基因型来检测和筛选假定的并行序列变异（PSVs）和多序列变异（MSVs）。总体而言，在彩虹鳟基因组29个染色体上共鉴定出30,302,087个SNPs，在未定位的构建体上鉴定出1,139,018个SNPs，其中4,042,723个SNPs具有高等位基因频率（MAF > 0.25）。染色体上的平均SNP密度为每64碱基一个SNP，或每1 kb 15.6个SNPs。我们进行的系统发育分析结果表明，尽管样本量较小，但SNP标记中包含足够的人口特异性多态性，可以恢复种群关系。种群内多态性评估揭示了每个种群内都存在高水平的多态性和杂合性。我们还基于每个SNP的基因组位置提供了功能注释，并评估了克隆系在筛选PSVs和MSVs中的应用。这些SNPs形成了一个新的数据库，为设计新的高密度SNP芯片以及用于该标志性鲑科鱼类遗传和基因组学研究的其他SNP基因分型平台提供了重要资源。