Data from: A novel approach to wildlife transcriptomics provides evidence of disease-mediated differential expression and changes to the microbiome of amphibian populations

Ranaviruses are responsible for a lethal, emerging infectious disease in
amphibians and threaten their populations throughout the world. Despite
this, little is known about how amphibian populations respond to ranaviral
infection. In the United Kingdom, ranaviruses impact the common frog (Rana
temporaria). Extensive public engagement in the study of ranaviruses in
the UK has led to the formation of a unique system of field sites
containing frog populations of known ranaviral disease history. Within
this unique natural field system, we used RNA sequencing (RNA-Seq) to
compare the gene expression profiles of R. temporaria populations with a
history of ranaviral disease and those without. We have applied a RNA read
filtering protocol that incorporates Bloom filters, previously used in
clinical settings, to limit the potential for contamination that comes
with the use of RNA-Seq in non-laboratory systems. We have identified a
suite of 407 transcripts that are differentially expressed between
populations of different ranaviral disease history. This suite contains
genes with functions related to immunity, development, protein transport
and olfactory reception amongst others. A large proportion of potential
non-coding RNA transcripts present in our differentially expressed set
provides first evidence of a possible role for long non-coding RNA
(lncRNA) in amphibian response to viruses. Our read-filtering approach
also removed significantly more bacterial reads from libraries generated
from postitive disease history populations. Subsequent analysis revealed
these bacterial read sets to represent distinct communities of bacterial
species, which is suggestive of an interaction between ranavirus and the
host microbiome in the wild.