Show simple item record Donaldson, Michael E. Rico, Yessica Hueffer, Karsten Rando, Halie M. Kukekova, Anna V. Kyle, Christopher J.
dc.coverage.spatial Alaska
dc.coverage.spatial USA 2017-12-06T22:26:15Z 2017-12-06T22:26:15Z 2017-12-02
dc.identifier doi:10.5061/dryad.f81c5
dc.identifier.citation Donaldson ME, Rico Y, Hueffer K, Rando HM, Kukekova AV, Kyle CJ (2017) Development of a genotype-by-sequencing immunogenetic assay as exemplified by screening for variation in red fox with and without endemic rabies exposure. Ecology and Evolution, online in advance of print.
dc.description Pathogens are recognized as major drivers of local adaptation in wildlife systems. By determining which gene variants are favored in local interactions among populations with and without disease, spatially explicit adaptive responses to pathogens can be elucidated. Much of our current understanding of host responses to disease comes from a small number of genes associated with an immune response. High-throughput sequencing (HTS) technologies, such as genotype-by-sequencing (GBS), facilitate expanded explorations of genomic variation among populations. Hybridization-based GBS techniques can be leveraged in systems not well characterized for specific variants associated with disease outcome to “capture” specific genes and regulatory regions known to influence expression and disease outcome. We developed a multiplexed, sequence capture assay for red foxes to simultaneously assess ~300-kbp of genomic sequence from 116 adaptive, intrinsic, and innate immunity genes of predicted adaptive significance and their putative upstream regulatory regions along with 23 neutral microsatellite regions to control for demographic effects. The assay was applied to 45 fox DNA samples from Alaska, where three arctic rabies strains are geographically restricted and endemic to coastal tundra regions, yet absent from the boreal interior. The assay provided 61.5% on-target enrichment with relatively even sequence coverage across all targeted loci and samples (mean = 50×), which allowed us to elucidate genetic variation across introns, exons, and potential regulatory regions (4,819 SNPs). Challenges remained in accurately describing microsatellite variation using this technique; however, longer-read HTS technologies should overcome these issues. We used these data to conduct preliminary analyses and detected genetic structure in a subset of red fox immune-related genes between regions with and without endemic arctic rabies. This assay provides a template to assess immunogenetic variation in wildlife disease systems.
dc.relation.haspart doi:10.5061/dryad.f81c5/1
dc.relation.haspart doi:10.5061/dryad.f81c5/2
dc.relation.haspart doi:10.5061/dryad.f81c5/3
dc.relation.isreferencedby doi:10.1002/ece3.3583
dc.subject arctic rabies virus
dc.subject immunogenomics
dc.subject local adaptation
dc.subject red fox
dc.subject sequence capture
dc.subject wildlife disease
dc.title Data from: Development of a genotype-by-sequencing immunogenetic assay as exemplified by screening for variation in red fox with and without endemic rabies exposure
dc.type Article
dwc.ScientificName Vulpes vulpes
dwc.ScientificName Vulpes lagopus
dc.contributor.correspondingAuthor Donaldson, Michael
prism.publicationName Ecology and Evolution

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Title Red fox immune-gene sequences
Downloaded 2 times
Description Red fox immune-gene sequences (2,229,152 bp) used to design the sequence capture assay.
Download red_fox_immune-gene_sequences.fasta (2.269 Mb)
Details View File Details
Title Red fox immune-gene SNPs
Downloaded 2 times
Description Red fox SNP variant call information.
Download red_fox_immune-gene_SNPs.vcf (32.88 Mb)
Details View File Details
Title Red fox NimbleGen SeqCap EZ_probes
Downloaded 2 times
Description Coordinates used to design the overlapping NimbleGen SeqCap EZ probes.
Download red_fox_NimbleGen_SeqCap_EZ_probes.bed (54.99 Kb)
Details View File Details

Search for data

Be part of Dryad

We encourage organizations to: