High quality Chromosome-scale Genome Assembly of Phlebotomus perniciosus, a Vector of Zoonotic Leishmaniasis.

Phlebotomus perniciosus is a major sand fly in the Western Mediterranean and a primary vector for Leishmania infantum, causing human and canine visceral leishmaniasis. This species can also transmit phleboviruses, including Toscana virus, associated with meningitis and encephalitis. Despite its importance, genomic resources for P. perniciosus remain limited, with only a low-quality assembly available. A high-quality reference genome is essential to study traits related to vector competence, host preference, and responses to control measures. Here, we present a high-quality de novo assembly using Oxford Nanopore long-read sequencing. We evaluated two assembly strategies, guided and unguided, using Canu and Flye. The guided Canu assembly was optimal, producing a 143 Mb genome with scaffold N50 of 48 Mb and 95% BUSCO completeness. Annotation with RNA-seq and protein homology predicted 12,492 genes (96% BUSCO) and 24% repetitive sequences. The complete mitochondrial genome was also assembled. This robust genome offers a foundation for investigating vector biology and adaptive traits, expanding genomic resources for phlebotomine sand flies and supporting improved leishmaniasis surveillance and control efforts.