Characterization of the Gray Whale Eschrichtius robustus Genome and a Genotyping Array Based on Single-Nucleotide Polymorphisms in Candidate Genes

• Published in: The Biological bulletin (Lancaster) Vol. 232; no. 3; p. 186
• Main Authors: 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
• Format: Journal Article
• Language: English
• Published: United States 01.06.2017
• Subjects: Animals; Genetic Variation; Genetics, Population; Genome - genetics; Genotype; Polymorphism, Single Nucleotide - genetics; Species Specificity; Whales - genetics; HWE, Hardy-Weinberg equilibrium; EGW, eastern gray whale; LD, linkage disequilibrium; STA, specific target amplification; IWC, International Whaling Commission; PE, paired end; PCR, polymerase chain reaction; SNP, single-nucleotide polymorphism; WGW, western gray whale; EST, expressed sequence tag; MP, mate paired; IUCN, International Union for Conservation of Nature
• ISSN: 1939-8697
• DOI: 10.1086/693483

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.