Data from: Characterization of the gray whale Eschrichtius robustus genome and a genotyping array based on single-nucleotide polymorphisms in candidate genes

Genetic and genomic approaches have much to offer in terms of ecology, evolution, and conservation. To better understand the biology of the gray whale Eschrichtius robustus (Lilljeborg, 1861), we sequenced the genome and produced an assembly that contains ∼95% of the genes known to be highly conserved among eukaryotes. From this assembly, we annotated 22,711 genes and identified 2,057,254 single-nucleotide polymorphisms (SNPs). Using this assembly, we generated a curated list of candidate genes potentially subject to strong natural selection, including genes associated with osmoregulation, oxygen binding and delivery, and other aspects of marine life. From these candidate genes, we queried 92 autosomal protein-coding markers with a panel of 96 SNPs that also included 2 sexing and 2 mitochondrial markers. Genotyping error rates, calculated across loci and across 69 intentional replicate samples, were low (0.021%), and observed heterozygosity was 0.33 averaged over all autosomal markers. This level of variability provides substantial discriminatory power across loci (mean probability of identity of 1.6 × 10−25 and mean probability of exclusion >0.999 with neither parent known), indicating that these markers provide a powerful means to assess parentage and relatedness in gray whales. We found 29 unique multilocus genotypes represented among our 36 biopsies (indicating that we inadvertently sampled 7 whales twice). In total, we compiled an individual data set of 28 western gray whales (WGSs) and 1 presumptive eastern gray whale (EGW). The lone EGW we sampled was no more or less related to the WGWs than expected by chance alone. The gray whale genomes reported here will enable comparative studies of natural selection in cetaceans, and the SNP markers should be highly informative for future studies of gray whale evolution, population structure, demography, and relatedness.遗传学与基因组学方法在生态学、进化生物学及物种保护领域具有极高的应用价值。为深入了解灰鲸（Eschrichtius robustus, Lilljeborg, 1861）的生物学特性，我们对其基因组进行了测序并构建了基因组组装版本，该组装覆盖了真核生物中已知95%的高度保守基因。基于该组装结果，我们共注释得到22711个蛋白编码基因，并鉴定出2057254个单核苷酸多态性位点（single-nucleotide polymorphisms, SNPs）。利用该组装结果，我们筛选得到一批受强烈自然选择作用的候选基因清单，涵盖渗透调节、氧结合与转运以及其他海洋生物适应性相关的基因。基于上述候选基因，我们采用由96个单核苷酸多态性位点组成的分型检测组合，其中包含2个性别鉴定标记与2个线粒体标记，对92个常染色体蛋白编码遗传标记位点进行了分型分析。通过对所有位点及69个预设重复样本的计算，分型错误率仅为0.021%；所有常染色体标记的平均观测杂合度为0.33。该变异水平赋予这些标记极强的位点区分能力：在未知双亲的情况下，平均个体识别概率为1.6×10⁻²⁵，平均排除概率大于0.999，表明该标记组合可有效用于灰鲸的亲权鉴定与亲缘关系分析。在36份皮肤活检样本中，我们共得到29种独特的多位点基因型，说明我们意外重复采样了7头灰鲸。最终我们共整理得到28头西灰鲸（Western Gray Whales, WGS）与1头疑似东灰鲸（Eastern Gray Whale, EGW）的个体数据集。我们采样的唯一一头东灰鲸与西灰鲸种群的亲缘关系完全符合随机预期水平。本研究报道的灰鲸基因组将为鲸类自然选择的比较研究提供支撑，而上述单核苷酸多态性标记也将在未来灰鲸进化、种群结构、种群动态及亲缘关系相关研究中展现出极高的应用价值。