Transcriptional profiling of Ivermectin resistant Cooperia punctata using deep sequencing.

<p>Intestinal parasites pose a burden to the livestock industry throughout the world. Since the discovery of macrocyclic lactones, Ivermectin has been a popular choice to combat nematode (roundworm) infectious due to its broad spectrum of action and high efficacy. Widespread use of this drug has led to the development of resistance in many parasitic nematodes, including the highly prevalent cattle intestinal parasite <em>Cooperia punctata</em>. Ivermectin is known to bind and activate glutamate-gated chloride channels, thereby disrupting neurotransmission and paralyzing the worms. We hypothesize that Ivermectin treatment of drug-resistant <em>C. punctata</em> will lead to changes in the expression pattern of genes related to the drugs mode of action. We used high throughput sequencing to study the adult transcriptome of drugresistant <em>C. punctata</em> and to assess Ivermectin’s impact on gene expression. RNAseq datasets from treated and untreated Ivermectin resistant adult worms were assembled into 110,772 unique transcripts corresponding to 66,788 genetic loci. 18,585 loci showed evidence of alternative splicing, with an average of 4 transcripts per alternatively spliced locus. Fragmentation rate was estimated at 18.1% by comparison with <em>C. elegans</em> CDSs. 101,411 CDSs, representing some 69% of the complete <em>C. punctata</em> gene repertoire, were predicted from our dataset. The predicted CDSs are associated with 4,738 unique InterPro protein domains, 3,013 unique Kyoto Encyclopedia of Gene and Genomes (KEGG) terms, and 524 unique Gene Ontology (GO) terms. 5,308 predicted CDSs were up-regulated in Ivermectin treated worms while 4,047 were down-regulated. Thirteen GO terms were statistically over-represented among up-regulated CDSs, including gated channels and metabolism. This suggests that functions related to Ivermectin’s mode of action are up-regulated in response to treatment. These results provide insights into potential mechanisms of Ivermectin resistance and possible genetic markers that may be used to monitor the spread of resistant <em>C. punctata</em> in cattle and prevent treatment failures.</p>