Development of high-quality reference genomes for Anopheles squamosus and An. cydippis

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Project Summary Despite the tremendous effort to minimize the impacts of malaria in southern Africa, it has yet to be eliminated from this region. Many understudied mosquito vector species inhabit this area and may be perpetuating malaria transmission in this pre-elimination zone. Anopheles squamosus is one of the most abundantly caught mosquito species in southern Zambia. This species is also frequently infected with Plasmodium falciparum, a causal agent of human malaria, leading to the hypothesis that it is a critical vector of malaria transmission in Zambia. A major barrier of testing this hypothesis and studying An. squamosus is the lack of genetic information. In addition to this barrier, An. squamosus is indistinguishable from An. cydippis in the adult stage, making it difficult to establish links between genotypes to phenotypes important for parasite transmission and vector control, including vector competence, insecticide resistance, and host preference. This study addresses these two key barriers by (1) producing high-quality genomes of An. squamosus and An. cydippis, (2) identifying genetic polymorphisms within An. squamosus, and (3) producing gene annotation of An. squamosus genome. The genome of An. squamosus will facilitate the identification of species-specific markers for a diagnostic assay that can be used to distinguish this species from other mosquitoes. Our project will catalyze the study of An. squamosus and other understudied malaria vectors, as well as their impacts on malaria transmission. The new genomic resources for An. squamosus can be leveraged for studying mosquito vector behavior and devise effective control strategies of understudied malaria vectors in pre-elimination settings.