Hypoderma spp. larvae cause internal myiasis in domestic and wild animals characterized by subcutaneous warbles. Their differentiation is usually performed at species level based on the morphology of third stage larvae. The recent release of the whole mtDNA of Hypoderma lineatum and the retrieval of a 102 bp noncoding region occurring between tRNA(Ser) and NADH dehydrogenase subunit 1 (nd1) genes represented the foundation for this study. The noncoding region and the two flanking mitochondrial genes (i.e., tRNA(Ser) and nd1) of the most diffused Hypoderma spp. (i.e., Hypoderma actaeon, Hypoderma bovis, Hypoderma diana, H. lineatum, Hypodermasinense and Hypoderma tarandi) were analysed. Interspecific variations in amplicon size (from 20 to 102 bp in H. tarandi and H. lineatum, respectively) and nucleotide sequences allowed a genetic discrimination of the examined species providing information instrumental to a rapid molecular identification of Hypoderma spp.
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