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

Abstract

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.

High‐quality whole‐genome sequence of an abundant Holarctic odontocete, the harbour porpoise (Phocoena phocoena)

“…The draft annotation using maker2 resulted in a total of 22,154 annotated genes. This number is comparable to other published cetacean genomes (Table ), including 21,459 genes predicted in the bottlenose dolphin (Lindblad‐Toh et al., ), 20,605 genes predicted in the minke whale (Yim et al., ), and 22,711 predicted genes in the grey whale (DeWoody et al., ). The annotated genes appear to broadly span key functional gene categories (biological processes, cellular components and molecular function, Figure ), both across the annotated GO terms and the interproscan results.…”

“…Genetic resources available for cetaceans do not yet adequately cover the diversity of this group (Foote et al., ; Keane et al., ; Nery et al., ; Sun et al., ; Yim et al., ; Zhou et al., ). Thus far, sequenced genomes include at least three baleen whales (DeWoody et al., ; Kishida et al., ; Yim et al., ) and six species of the toothed whales (Foote et al., ; Jones et al., ; Lindblad‐Toh et al., ; Neely et al., ; Warren et al., ; Yuan et al., ; Zhou et al., , ). While the number of available genomes is growing rapidly, they do not fully represent extant taxa, and the completeness of their assemblies varies (Table ).…”

Genetic and genomic monitoring with minimally invasive sampling methods

“…The fisheries community has embraced SNP genotyping assaying scores of loci with the Fluidigm platform (Bonanomi, Therkildsen, Retzel, & Berg, ; Campbell & Narum, ; Hauser, Baird, Hilborn, Seeb, & Seeb, ), and recently, several wildlife studies have also used this platform in a monitoring context (Table : Doyle et al., ; Kraus et al., ; Nussberger, Wandeler, & Camenisch, ). The Fluidigm SNP type assay seems to have relatively low error rates (e.g., 0.2% in DeWoody et al., ; 0.4% in Doyle et al., ; where error rates are estimated from the number of mismatches between replicates and consensus genotype; 1%–3% per allele in Kraus et al., ; 1.7% per locus in Nussberger et al., ). The low error rate is important for all aspects of molecular ecology, but particularly for inferences of individual identification, parentage and relatedness.…”

Estimating effective population size of large marine populations, is it feasible?

“…In the past, N e was considered difficult to estimate but this situation has changed (Leberg, ; Schwartz, Tallmon, & Luikart, ). As a consequence, N e is nowadays commonly estimated for varied marine taxa: mammals (DeWoody et al., ), crustaceans (Watson, McKeown, Coscia, Wootton, & Ironside, ), corals (Holland, Jenkins, & Stevens, ) and fishes (Laconcha et al., ; Pita, Pérez, Velasco, & Presa, ; Zhivotovsky et al., ). Among commercial fish species, both target (Montes et al., ; Poulsen, Nielsen, Schierup, Loeschcke, & GrøNkjaer, ) and by‐catch species (Chevolot, Ellis, Rijnsdorp, Stam, & Olsen, ) have been studied, representing a wide range of life history strategies, habitats, population structures but also census population sizes (i.e., total number of individuals in the population including immatures, denoted N ), from hundreds to billions of individuals.…”