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. ...

遗传学与基因组学研究方法在生态学、进化生物学及保护生物学领域具有重要应用价值。为深入解析灰鲸（Eschrichtius robustus, Lilljeborg, 1861）的生物学特征，本研究对其基因组进行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）。通过该基因组组装，我们构建了一套经过人工整理校正的候选基因列表，这些候选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生理过程相关的基因。基于上述候选基因，我们采用包含96个单核苷酸多态性位点的标记组合（其中涵盖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标记进行了靶向分析。通过对所有位点以及69个预设重复样本进行计算，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。……