The disease chytridiomycosis caused by the fungus Bd has devastated amphibian populations worldwide. Functional genomic contributions to host susceptibility remain enigmatic and vary between species and populations. We conducted experimental Bd infections in Rana yavapaiensis, a species with intraspecific variation in chytridiomycosis susceptibility, to assess the skin and spleen transcriptomic response to infection over time. We predicted that increased immune gene expression would be associated with a positive disease outcome, but we instead found that surviving frogs had significantly reduced immune gene expression compared to susceptible frogs and to uninfected controls. MHC class II gene expression was also significantly higher in susceptible frogs compared to surviving frogs. Furthermore, susceptible frogs expressed a significantly larger number of distinct class II alleles, demonstrating a negative correlation between class II expression, functional diversity, and survival. Expression of the MHC class II locus previously associated with Bd disease outcomes was a significant predictor of Bd infection intensity at early infection stages but not at late infection stages, suggesting initial MHC-linked immune processes are important for ultimate disease outcomes. We infer through disease association and phylogenetic analysis that certain MHC variants are linked to the immune expression that was negatively associated with survival, and we hypothesize that frogs that did not express these alleles could better survive infections. Our study finds that MHC expression at early and late infection stages predicts Bd infection intensity, and suggests that generating a sustained immune response against Bd may be counterproductive for surviving chytridiomycosis in this partially susceptible species.

This dataset presents replicate qPCR pathogen quatification values for control and Bd-exposed individuals that were lab-reared from egg masses through metamorphosis and tracked for a 55 day exposure experiement.

All control and Bd-exposed individuals were housed in separate cages and swabbed weekly, as well as swabbed at the time of euthanasia when RNAseq tissues were also collected. DNA was extracted from swabs and standard Bd qPCR protocols were used to run each sample in duplicate. Serial dilutions of known quantities of the pathogen were included as stadards, enabling absolute pathogen quantification.