Generating transcriptome resources for the rumen fluke, Calicophoron daubneyi.

Infections by parasitic flatworms are an important animal health and production concern for livestock producers worldwide. In recent years there has been a sharp increase in both the incidence and severity of rumen fluke (the paramphistome Calicophoron daubneyi) infections in both sheep and cattle in Western Europe. This is a major concern since outbreaks of clinical (and fatal) paramphistomosis are on the rise in the UK/Ireland. Despite their prevalence, our current knowledge of basic rumen fluke biology, and how they interact with their hosts, is remarkably limited. To begin to address this, we have generated significant transcriptome datasets for C. daubneyi via long read PacBio sequencing which served as a reference map for differential expression analysis (Illumina RNAseq) of 4 intra-mammalian life-cycle stages: newly excysted juveniles, immature worms recovered from the small intestine, newly-migrated flukes and adults, both recovered from the rumen. It is envisaged that these resources will aid discovery of novel vaccine candidates and diagnostic antigens for this emerging parasite infection.