Gopherus polyphemus immune gene URTD. Gopherus polyphemus

Immune response genes control the immune system's response to pathogens and because changes in these genes can alter disease susceptibility, they are likely to be influenced by natural selection and potentially affect population viability. Populations of threatened species generally possess low levels of genetic variation, and genetically depauperate hosts may be at greater risk of infectious disease contributing to extirpations. To better understand the genetic basis of infectious disease susceptibility in a species of conservation concern, we sequenced the immune response genes (i.e., immunomes) from 16 free-ranging gopher tortoises Gopherus polyphemus from 3 Florida populations (CF, FC, and OLD) with (n=10) or without (n=6) clinical symptoms and that produced antibodies against one of causal agents for an infectious upper respiratory tract disease (URTD). We found one non-synonymous SNP unique to all but one URTD symptomatic tortoise (a subclinical animal observed twice, once with URTD symptoms and again without). We found genetic diversity was lowest in CF followed by OLD and FC. Population differentiation and admixture were as expected based on geographic proximity of the populations. There were two SNPs putatively under selection according to FST outlier tests, and there were 35 genes that deviated from neutrality according to Tajima's D. Functional enrichment analysis of these genes showed overrepresentation of several functions: endoplasmic reticulum, cellular protein modification processes, macromolecule modification, and transferase activity. These results demonstrate that immunome sequencing can be conducive to better understanding the genetic basis of infectious disease and can provide valuable information on selection and genetic diversity.