Gopherus polyphemus immune gene

Genetic diversity at functional genes such as those involved in immune responses can influence individual fitness and population viability. Populations of threatened species typically have low overall genetic diversity and are depauperate in immunogenetic variation, which can negatively influence disease susceptibility. Most studies of immunogenetic variation in the threatened wildlife have focused on a handful of genes, but genomic resources and next-generation sequencing now enable researchers to assess hundreds of immune genes simultaneously. In this study, we filtered the genome of the western painted turtle for genes involved in immune response (i.e., the immunome) and then designed reagents to acquire these genes from a species of conservation concern, the gopher tortoise (Gopherus polyphemus), to better understand the genetic basis of disease susceptibility. Gopher tortoises are associated with long-leaf pine forests of the southeastern United States and are susceptible to an infectious and occasionally deadly upper respiratory tract disease. We sequenced the immunomes of 16 gopher tortoises from 4 populations along an east to west gradient covering the range of the species and assessed population genetic diversity and differentiation. Nearly all desired genomic regions were represented, and we obtained approximately 20,000 variable single nucleotide polymorphism (SNP) loci. Population genetic diversity and differentiation estimated with SNP loci paralleled patterns previously inferred by genotyping more than 19 tortoises per population using 10 microsatellite loci. Further work will involve sequencing immunomes from healthy and sick gopher tortoises to better understand what genetic variants are associated with susceptibility to upper respiratory tract disease. Our study illustrates the effectiveness of immunome sequencing as a practical tool for not only population but also conservation genomics.