The equine pinworm Oxyuris equi (Nematoda: Oxyuridomorpha) is the most common horse nematode, has a worldwide distribution, and causes major economic losses. In the present study, the complete O. equi mitochondrial (mt) genome was sequenced, and the mt genome structure and organization were compared with those of other closely related pinworm species, Enterobius vermicularis and Wellcomia siamensis. The O. equi mt genome is a 13,641-bp circular DNA molecule that encodes 36 genes (12 protein-coding genes, 22 tRNAs, and two rRNAs) and one non-coding region, which is slightly shorter than that of E. vermicularis and W. siamensis. The O. equi mt gene arrangement was consistent with that of GA13-type E. vermicularis but it differs from GA12-type W. siamensis. Phylogenetic analyses using concatenated amino acid sequences of the 12 protein-coding genes with three different computational algorithms (maximum parsimony, maximum likelihood, and Bayesian inference) revealed that there were two distinct clades in Chromadorea nematodes that reflected infraorder. Spiruromorpha formed one clade, whereas Rhabditomorpha, Ascaridomorpha, and Oxyuridomorpha formed another clade. O. equi, E. vermicularis, and W. siamensis represent distinct but closely related species, which indicated that Oxyuridomorpha is paraphyletic. Sequencing the O. equi mt genome provides novel genetic markers for studying the molecular epidemiology and population genetics of pinworms.
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