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.

蛙病毒（Ranavirus）可引发两栖动物致死性新发传染病，对全球两栖动物种群构成严重威胁。尽管如此，学界对两栖动物种群应对蛙病毒感染的响应机制仍缺乏深入了解。在英国，蛙病毒会侵染普通蛙（Rana temporaria）。英国公众广泛参与蛙病毒相关研究，催生了一套独特的野外研究体系：该体系涵盖了已知蛙病毒感染病史的蛙类种群野外采样位点。在这套独特的自然野外研究体系中，我们借助RNA测序（RNA-Seq）技术，对比了有蛙病毒感染病史与无感染病史的普通蛙（Rana temporaria）种群的基因表达谱。我们采用了一种结合布隆过滤器（Bloom filter）的RNA读段过滤方案——该过滤器此前已应用于临床场景——以降低非实验室环境下开展RNA测序时可能出现的污染风险。我们共筛选得到407个转录本，它们在不同蛙病毒感染病史的种群间呈现差异表达。该差异表达转录本集合涵盖了与免疫、发育、蛋白质转运及嗅觉接收等功能相关的基因。该差异表达集合中存在大量潜在非编码RNA转录本，为长链非编码RNA（long non-coding RNA, lncRNA）在两栖动物抗病毒应答中发挥潜在作用提供了首项实验证据。我们的读段过滤方案还从感染病史阳性的种群构建的测序文库中，显著去除了更多的细菌读段。后续分析显示，这些细菌读段对应着不同的细菌物种群落，这暗示野外环境中蛙病毒与宿主微生物组之间存在相互作用。