Uncinaria stenocephala and Ancylostoma caninum genome skimming
This project applied genome skimming to recover mitochondrial genomes (mitogenomes) of two common canine hookworms, Ancylostoma caninum and Uncinaria stenocephala, directly from faecal egg isolates and cultured larvae. Genome skimming involves shallow whole-genome sequencing of mixed DNA samples, enabling efficient recovery of high-copy organellar genomes without the need for parasite isolation. Using Illumina NovaSeq 6000 sequencing, we assembled complete or near-complete mitogenomes from dog-derived U. stenocephala eggs and A. caninum larvae. Comparative mapping confirmed high coverage and sequence identity with reference mitogenomes, demonstrating the feasibility of this approach for non-invasive sampling. The method proved effective even at low sequencing depths, allowing mitogenome reconstruction from faecal material where adult worms are inaccessible. These data contribute to expanding mitogenomic resources for hookworms and highlight genome skimming as a practical tool for molecular parasitology, taxonomy and surveillance.