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备极高的应用潜力。为深入解析灰鲸（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基因组组装版本，该组装覆盖了真核生物中已知约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（single-nucleotide polymorphisms, SNPs）。通过该组装，我们筛选得到一份经人工整理注释的候选基因列表，这些候选基因可能受到强烈自然选择作用，涵盖与渗透压调节、氧结合与转运及其他海洋生存相关性状的编码基因。我们从这些候选基因中筛选出92个常染色体蛋白编码遗传标记，并采用包含96个单核苷酸多态性的检测面板进行分型，该面板同时涵盖2个性别鉴定标记与2个线粒体标记。通过对所有基因座及69个预设重复样本的计算，本研究得到的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。该变异水平在各基因座间具备极强的鉴别能力（双亲未知时，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权关系与个体亲缘程度。我们在36份皮肤活检样本中鉴定出29种独特的多位点基因型，说明我们无意间重复采样了7头灰鲸。最终，我们共构建了包含28头西太平洋灰鲸（western gray whales, WGSs）与1头疑似东太平洋灰鲸（eastern gray whale, EGW）的个体数据集。本次采样得到的唯一一头疑似东太平洋灰鲸，与西太平洋灰鲸群的亲缘关系并未超出随机预期的范畴。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为未来灰鲸进化、种群结构、种群动态及亲缘关系相关研究提供高信息价值的研究工具。