Nuclear, mitochondrial, and <i>Wolbachia</i> endosymbiont genomes of <i>Onchocerca lupi</i>, Portugal

Zoonotic <i>Onchocerca lupi</i> (Spirurida, Onchocercidae) has attracted the interest of the scientific community worldwide, by causing severe ocular infections in domestic animals (dogs, cats) and can infect wild carnivores (wolves, coyotes), as well as humans. Though recent advancements in scientific knowledge have been gained, gaps still remain about the biology of this filarioid, as well as its genetic structure. Based on mitochondrial genes, two highly divergent genotypes were identified, in the Iberian Peninsula (genotype 2) and Europe, Asia, and the United States (genotype 1), meanwhile only a draft nuclear genome of <i>O. lupi</i> from the United States is available. This study aimed to fill knowledge gaps about the genomic characterization of this filarioid and its <i>Wolbachia</i> endosymbiont. This study described the shotgun sequencing of an adult specimen of <i>O. lupi</i> isolated from a dog living in Portugal using the PacBio long-read sequencing technology. Three distinct genomes, such as the nuclear, mitochondrial, and <i>Wolbachia</i> endosymbiont, were assembled and analyzed. The assembled nuclear genome, Olupi_PT2024, exhibited high contiguity, accuracy, and completeness. Pairwise mitogenome comparative analyses among several <i>Onchocerca</i> species corroborated the high divergence between the two genotypes from Portugal and the USA, although the observed differences remained within the range of intra-species variation. The complete genome of the <i>Wolbachia</i> endosymbiont of <i>O. lup</i>i confirmed its classification within supergroup C and its close phylogenetic relationship with <i>Wolbachia</i> endosymbionts associated with the genus <i>Onchocerca</i>. The data on these three genomes may provide valuable resources for understanding the biology, population genetics, and phylogeography of this parasite.IMPORTANCE<i>Onchocerca lupi</i>, a zoonotic parasite, causes ocular onchocerciasis in both domestic and wild carnivores, as well as humans. Despite recent scientific advances, gaps remain in both the biology and genetic structure of this parasite. To date, two genotypes have been described (genotype 1 distributed in Europe, Asia, and the United States, and genotype 2 circulating in the Iberian Peninsula) based on mitochondrial gene analysis. This study provided three distinct genomes (nuclear, mitochondrial, and <i>Wolbachia</i> endosymbiont) of <i>O. lupi</i> isolated from a dog living in Portugal. Overall, the data presented here corroborate the divergence between the two genotypes and provide new insights into the identification of genes that could serve as novel therapeutic targets for this filarial disease.