Data_Sheet_2_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。对于彩虹鲑（Oncorhynchus mykiss）而言，此前已通过限制性位点关联DNA（RAD）文库、减少代表性文库（RRL）以及RNA测序等技术实现了SNP的发现。近期，我们对61份无关样本进行了高覆盖度全基因组重测序，这些样本代表了一系列彩虹鲑和钢头鲑种群，其中新增49份样本，包括12份来自挪威AquaGen的养殖样本，这些样本先前已被用于SNP发现。在新增的49份样本中，有11份来自华盛顿州立大学（WSU）的双倍体纯合系，其余38份则代表了广泛地理分布的野生和养殖种群，并具有不同的迁徙表型。随后，我们将序列映射至新的彩虹鲑参考基因组组装（GCA_002163495.1），该组装基于Swanson YY双倍体纯合系。使用FreeBayes和SAMtools mpileup进行了变异调用，随后根据质量分数、序列复杂性、位点的读深以及基因型样本的数量对SNPs进行了筛选。对比了两种变异调用程序的结果，并利用双倍体样本的基因型来检测和筛选潜在的平行序列变异（PSVs）和多序列变异（MSVs）。总体而言，在彩虹鲑29条染色体上共发现了30,302,087个SNPs，在未定位的支架上发现了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标记仍包含足够的种群特异性多态性，可用于恢复种群关系。种群内多态性评估揭示了每个种群内部都存在高水平的多态性和杂合性。我们还根据每个SNP的基因组位置进行了功能注释，并评估了克隆系在筛选PSVs和MSVs中的应用。这些SNPs构成了一个新的数据库，为设计新的高密度SNP芯片提供了重要资源，并为用于该标志性鲑鱼物种遗传和基因组学研究的其他SNP基因分型平台提供了支持。