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 ...

• Main Authors: Donaldson, Michael E., Rico, Yessica, Hueffer, Karsten, Rando, Halie M., Kukekova, Anna V., Kyle, Christopher J.
• Format: Dataset
• Language: English
• Published: Dryad 2018
• Subjects: immunogenomics; arctic rabies virus; red fox; wildlife disease; Vulpes lagopus; Arctic
• Online Access: https://dx.doi.org/10.5061/dryad.f81c5; https://datadryad.org/stash/dataset/doi:10.5061/dryad.f81c5

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 ... : Red fox immune-gene sequencesRed fox immune-gene sequences (2,229,152 bp) used to design the sequence capture assay.red_fox_immune-gene_sequences.fastaRed fox immune-gene SNPsRed fox SNP variant call information.red_fox_immune-gene_SNPs.vcfRed fox NimbleGen SeqCap EZ_probesCoordinates used to design the overlapping NimbleGen SeqCap EZ probes.red_fox_NimbleGen_SeqCap_EZ_probes.bed ...