A SNP resource for studying North American moose

Abstract

Background: Moose ( Alces alces) colonized the North American continent from Asia less than 15,000 years ago, and spread across the boreal forest regions of Canada and the northern United States (US). Contemporary populations have low genetic diversity, due either to low number of individuals in the original migration (founder effect), and/or subsequent population bottlenecks in North America. Genetic tests based on informative single nucleotide polymorphism (SNP) markers are helpful in forensic and wildlife conservation activities, but have been difficult to develop for moose, due to the lack of a reference genome assembly and whole genome sequence (WGS) data. Methods: WGS data were generated for four individual moose from the US states of Alaska, Idaho, Wyoming, and Vermont with minimum and average genome coverage depths of 14- and 19-fold, respectively. Cattle and sheep reference genomes were used for aligning sequence reads and identifying moose SNPs. Results: Approximately 11% and 9% of moose WGS reads aligned to cattle and sheep genomes, respectively. The reads clustered at genomic segments, where sequence identity between these species was greater than 95%. In these segments, average mapped read depth was approximately 19-fold. Sets of 46,005 and 36,934 high-confidence SNPs were identified from cattle and sheep comparisons, respectively, with 773 and 552 of those having minor allele frequency of 0.5 and conserved flanking sequences in all three species. Among the four moose, heterozygosity and allele sharing of SNP genotypes were consistent with decreasing levels of moose genetic diversity from west to east. A minimum set of 317 SNPs, informative across all four moose, was selected as a resource for future SNP assay design. Conclusions: All SNPs and associated information are available, without restriction, to support development of SNP-based tests for animal identification, parentage determination, and estimating relatedness in North American moose.

Moose and Caribou as Novel Sources of Functional Lipids: Fatty Acid Esters of Hydroxy Fatty Acids, Diglycerides and Monoacetyldiglycerides

“…Cervids refer to animals of the Cervidae family and include species such as deer, elk, moose, and caribou. These species are popular big game species present throughout the circumpolar boreal forests of Eurasia and North America, such as Canada, Alaska, New England [29]. Though these species are typically wild and free ranging, in many countries they are farmed, and the meat used as high-quality protein sources [4], and the antlers used for medicinal purposes [12].…”

Genomic Underpinnings of Population Persistence in Isle Royale Moose

“…Whole-genome sequencing was performed on an Illumina NovaSeq at the Vincent J. Coates Genomics Sequencing Laboratory at University of California, Berkeley and MedGenome. Existing genomes from Kalbfleisch et al (2018) and Dussex et al (2020) were downloaded from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (see supplementary table S1, Supplementary Material online).…”

Genomic underpinnings of population persistence in Isle Royale moose

“…Whole-genome sequencing was performed on an Illumina NovaSeq at the Vincent J. Coates Genomics Sequencing Laboratory at University of California, Berkeley and MedGenome. Existing genomes from (61) and (30) were downloaded from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (see Table S1).…”