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极具应用价值。为深入理解灰鲸（*Eschrichtius robustus*, Lilljeborg, 1861）的生物学特性，本研究对其基因组进行测序并构建了基因组组装序列，该组装覆盖了真核生物中已知的约95%的高度保守基因。基于该组装序列，我们注释得到22711个基因，并鉴定出2057254个单核苷酸多态性（single-nucleotide polymorphisms, SNPs）。利用该组装序列，我们生成了一份经过人工校验筛选的候选基因列表，这些基因可能受到强烈的自然选择作用，其中包括与渗透压调节、氧结合与转运以及其他海洋生存相关特征相关的基因。从上述候选基因中，我们选取了92个常染色体蛋白编码标记位点，并构建了包含96个SNPs的分型检测面板，该面板额外包含2个性别鉴定标记与2个线粒体标记。通过对所有位点及69份重复对照样本的计算，基因分型错误率仅为0.021%；所有常染色体标记的平均观测杂合度为0.33。该变异水平使得这些位点具备极强的个体区分能力：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，表明这些标记可用于高效评估灰鲸的亲子关系与亲缘关联。在36份皮肤活检样本中，我们共鉴定出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。我们所采样的这头唯一东灰鲸，与西灰鲸种群的亲缘关系并未超出随机预期的范围。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，而本次开发的SNP标记也将为未来灰鲸进化、种群结构、种群动态及亲缘关系的相关研究提供极具价值的工具。