Genomic diversity of the horse strongyle Cylicocyclus nassatus

Cyathostomins are a complex of 50 intestinal parasite species infecting horses and wild equids. The massive administration of modern anthelmintic drugs has increased their relative abundance in horse helminth communities and selected drug-resistant isolates worldwide. Cylicocyclus nassatus is the most abundant and one of the most prevalent species. The tedious identification and isolation of these worms has hampered studies of their biology that remain largely uncharacterised. Here we have leveraged ultra-low input sequencing protocols to build a reference genome for the most prevalent horse strongyle species. Using this resource we have established the first estimates of its genetic diversity and population structure on a gradient ranging from Ukraine (close to modern horse domestication area) to North America, while capturing a XIXth century snapshot of C. nassatus diversity in Egypt. We identified the first genetic candidates upon which pyrantel - an anthelmintic drug used in companion animals - selection likely applies in field populations, highlighting previously suspected genes coding for nicotinic acetylcholine receptor subunits, and identifying new candidates replicated in evolved C. elegans lines. These results offer a first resource to widen current knowledge on cyathostomin biology, unravel novel aspects of pyrantel resistance mechanisms and provide candidate genes to track pyrantel resistance in the field.