Whole genome pool sequencing reveals genomic variation in field Haemonchus contortus isolates in Sweden

Abstract Background Haemonchus contortus is a major gastrointestinal parasite of small ruminants worldwide. Its large effective population size, high fecundity, and extensive genetic variation promote rapid adaptation and the development of anthelmintic resistance. Resolving genome-wide genetic variation in H. contortus within and among populations is essential for tracking variant distribution, interpreting resistance-associated markers, and informing parasite control strategies. Although reduced representation and targeted marker approaches have provided important insights into population structure, whole genome sequencing is required to fully characterise population differentiation. This study aimed to characterise genome-wide variation within and between field-derived H. contortus populations in Sweden, using whole genome sequencing of pools of individuals from 12 sheep farms. Results Field-derived H. contortus isolates from Swedish farms showed high genomic diversity within populations (nucleotide diversity (Pi) = 0.0211–0.0253) and relatively low genomic differentiation among most populations (fixation index (F ST ) < 0.1). However, three population pairs displayed higher genomic differentiation (F ST = 0.144–0.157) combined with lower genomic nucleotide diversity (Pi = 0.0211–0.0227), with divergence concentrated on chromosomes 4, 5, and X. Significantly differentiated single nucleotide polymorphisms were linked to a limited set of annotated genes involved in regulatory, signalling, and nervous system-related functions. However, the biological basis of these patterns remains unclear and will require further investigation using phenotype-linked data and farm-management metadata. Conclusions This work establishes the first genome-wide baseline for field-derived H. contortus populations across multiple Swedish sheep farms and shows that pooled-sample whole-genome sequencing (Pool-seq) is a useful method for describing broad population-genomic patterns in this species. Our findings indicate relatively low genomic variation between Swedish H. contortus populations and high genomic variation within them. This study provides a valuable foundation for future research on parasite adaptation, resistance, surveillance, and control.