Aedes aegypti is the vector of important human diseases, including the debilitating Dengue Fever virus. Because this mosquito has a broad global distribution and thrives in urban environments, it poses a grave risk to human health. Genomic resources are crucial in facilitating the study of Ae. aegypti and its interactions with its pathogens, ecological disturbances, and pesticide applications. Laboratory strains of Ae. aegypti were established at various times during the late 19th to mid-20th century, but the two most commonly used strains are Liverpool (LVP) and Rockefeller (ROCK), both established prior to widespread chemical pesticide use. A full-length genome assembly was sequenced from LVP and is the species reference genome (AaegL5.3). However, relevant differences in gene expression between LVP and ROCK have been known for decades. This indicates that the LVP reference genome is not fully representative of the ROCK genome, presenting potential impediments to research. Here we present a chromosomal-level assembly and annotation of the ROCK genome and a comparative characterization versus AaegL5.3 Our assembly of the ROCK genome is slightly longer than AaegL5.3 and provides evidence of potential structural variation and gene copy number differences. Our results set the stage for a pan-genomic approach to understanding evolution and diversity within this important disease vector. To illustrate the value of this approach, we present preliminary results of variant analysis using pool-seq of a pesticide-resistant strain and four ROCK-derived, pesticide-resistant congenic lines. Armed with two reference genomes of strains isolated before the evolution of pesticide resistance, we can better characterize fixed polymorphisms in resistant strains as tightly associated with resistance when we find them in the resistant strain but not in either susceptible strain.

Chromosome-level assembly of the “Rockefeller” Aedes aegypti mosquito strain powers investigation of the evolution of pesticide resistance in a vector of human and livestock disease

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ACS Fall 2022

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