TY - JOUR

T1 - Characterization of the Gray Whale Eschrichtius robustus Genome and a Genotyping Array Based on Single-Nucleotide Polymorphisms in Candidate Genes

AU - DeWoody, J. Andrew

AU - Fernandez, Nadia B.

AU - Brüniche-Olsen, Anna

AU - Antonides, Jennifer D.

AU - Doyle, Jacqueline M.

AU - Miguel, Phillip San

AU - Westerman, Rick

AU - Vertyankin, Vladimir V.

AU - Godard-Codding, Céline A. J.

AU - Bickham, John W.

N1 - Funding Information: We thank the International Whaling Commission (IWC) and Aimée Lang for curating the 2011 western gray whale samples provided via the IWC. This work was conducted under the National Marine Fisheries Service (NMFS) Office of Protected Resources’ Marine Mammal Health and Stranding Response Program permits 932-1905-MA-009526 and 18786 and Convention on the International Trade in Endangered Species of Wild Fauna and Flora permit 13US082589/9. This work was supported by Exxon Neftegas Limited and the Sa-khalin Energy Investment Company. Both collaborative agencies and funding parties received annual progress reports for the past several years. The content presented here is solely the responsibility of the authors and does not necessarily represent the official views of the funding parties. We also thank Teri Rowles (NMFS) for assistance with the project. A. Aziz, J. Dupont, M. Scott, and M. Swindoll provided support in obtaining the biopsies and associated metadata. The Institute of Ecology and Evolution of the Russian Academy of Sciences, the A. V. Zhirmunsky Institute of Marine Biology Far Eastern Branch, and Oregon State University provided invaluable support for the collection of the western gray whale samples. We thank E. Srour and A. Cardoso (Indiana University School of Medicine) for laboratory assistance and support. C. George and R. Suydam (Department of Wildlife Management, North Slope Borough of Alaska) provided the putative eastern gray whale samples. Finally, we thank S. Fears, Y. Ji, M. Sundaram, and J. Willoughby for constructive comments. Publisher Copyright: © 2017 The University of Chicago.

PY - 2017

Y1 - 2017

N2 - 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 os-moregulation, 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. Genotyp-Genotyp-ing error rates, calculated across loci and across 69 intentional replicate samples, were low (0.021%), and observed het-erozygosity 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 ing 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.

AB - 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 os-moregulation, 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. Genotyp-Genotyp-ing error rates, calculated across loci and across 69 intentional replicate samples, were low (0.021%), and observed het-erozygosity 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 ing 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.

U2 - 10.1086/693483

DO - 10.1086/693483

M3 - Journal article

C2 - 28898601

AN - SCOPUS:85029599288

VL - 232

SP - 186

EP - 197

JO - Biological Bulletin

JF - Biological Bulletin

SN - 0006-3185

IS - 3

ER -