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.

蛙病毒属病毒（Ranaviruses）可引发两栖动物致死性新发传染病，并对全球范围内的两栖动物种群构成威胁。尽管如此，学界对两栖动物种群如何应对蛙病毒感染仍知之甚少。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，促成了一套独特的野外研究站点体系，这些站点内的蛙种群均已知晓其蛙病毒感染病史。依托这套独特的天然野外研究体系，我们采用RNA测序（RNA sequencing, 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种群的基因表达谱。我们采用了一种整合了布隆过滤器（Bloom filters）的RNA读段过滤方案——该过滤器此前已应用于临床场景——以规避非实验室环境下开展RNA-Seq时可能出现的污染问题。我们共鉴定出407个转录本，其在不同蛙病毒感染病史的普通蛙种群中存在差异表达。该差异表达转录本集合涵盖了与免疫、发育、蛋白质转运及嗅觉感知等相关功能的基因。差异表达集合中存在大量潜在非编码RNA转录本，这为长链非编码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个证据。我们的读段过滤方案还显著去除了更多来自阳性感染病史种群构建的测序文库中的细菌读段。后续分析表明，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。