Comparative Mitogenomics Reveals Mitochondrial Diversity of Haemonchus contortus, a Major Gastrointestinal Parasite of Ruminants

Haemonchus contortus is a highly pathogenic hematophagous gastrointestinal nematode and one of the most important constraints to small-ruminant health and productivity worldwide, causing anemia, reduced weight gain, decreased milk production, and substantial economic losses. Understanding its genetic diversity and population structure is essential for improving parasite surveillance and informing sustainable control strategies. In this study, individual H. contortus larvae collected from Pakistani livestock were subjected to whole-genome sequencing, and complete mitochondrial (mt) genomes were assembled and analyzed using comparative mitogenomics, phylogenetic reconstruction, pairwise genetic distance estimation, and haplotype network analyses. Forty-one H. contortus larvae were successfully characterized for their mitochondrial genomes. The first complete mitochondrial genome of Pakistani H. contortus was 14,002 bp in length and comprised 12 protein-coding genes, 22 transfer RNA genes, and two ribosomal RNA genes, with a marked AT content of 78.37%. Mitochondrial genome organization and gene order were highly conserved relative to published H. contortus mitogenomes. Comparative analyses resolved the Pakistani isolates into two well-supported mitochondrial lineages, while maximum-likelihood phylogenetic analysis clustered all isolates within a robust H. contortus clade clearly distinct from H. placei (bootstrap support, 97–100%). Pairwise genetic distances among Pakistani isolates ranged from 0.00 to 0.05, indicating pronounced nucleotide divergence. Haplotype network analysis identified numerous unique haplotypes together with globally shared haplotypes, supporting substantial mitochondrial diversity. Collectively, these findings provide the first complete mitogenomic resource for H. contortus from Pakistan and advance our understanding of the genetic structure of this economically important veterinary parasite. The generated genomic resource will support molecular epidemiology, population genetic studies, veterinary parasite surveillance, and future investigations of parasite dissemination and anthelmintic resistance in ruminant production systems.