DeWoody J Andrew, Fernandez Nadia B, Brüniche-Olsen Anna, Antonides Jennifer D, Doyle Jacqueline M, San Miguel Phillip, Westerman Rick, Vertyankin Vladimir V, Godard-Codding Céline A J, Bickham John W
Biol Bull. 2017 Jun;232(3):186-197. doi: 10.1086/693483. Epub 2017 Sep 1.
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 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.
遗传和基因组方法在生态学、进化和保护方面有很多贡献。为了更好地了解灰鲸（Eschrichtius robustus，Lilljeborg，1861）的生物学特性，我们对其基因组进行了测序，并生成了一个包含约95%已知在真核生物中高度保守基因的组装体。从这个组装体中，我们注释了22,711个基因，并鉴定出2,057,254个单核苷酸多态性（SNP）。利用这个组装体，我们生成了一份经过筛选的潜在受到强烈自然选择的候选基因列表，包括与渗透调节、氧气结合和运输以及海洋生活其他方面相关的基因。从这些候选基因中，我们用一组96个SNP对92个常染色体蛋白质编码标记进行了查询，其中还包括2个性别鉴定标记和2个线粒体标记。在所有位点和69个有意重复样本中计算的基因分型错误率很低（0.021%），所有常染色体标记的平均观察杂合度为0.33。这种变异水平在各个位点提供了强大的鉴别能力（平均个体识别概率为1.6×10，在双亲均未知的情况下平均排除概率>0.999），表明这些标记为评估灰鲸的亲子关系和亲缘关系提供了有力手段。我们在36份活检样本中发现了29种独特的多位点基因型（表明我们无意中对7头鲸鱼进行了两次采样）。总共，我们编制了一个包含28头西部灰鲸（WGS）和1头推定东部灰鲸（EGW）的个体数据集。我们采样的这头单独的EGW与WGW的亲缘关系不比仅由随机因素预期的更密切或更疏远。这里报道的灰鲸基因组将有助于对鲸类自然选择进行比较研究，并且这些SNP标记对于未来灰鲸进化、种群结构、种群统计学和亲缘关系的研究应该具有很高的信息量。
