Genome Assembly and Molecular Genetics of the Dengue, Yellow Fever, and Zika Vector Aedes Aegypti

The mosquito Aedes aegypti is a potent and deadly vector of arboviruses, including Zika, Chikungunya, dengue, and yellow fever. Increasingly, mosquito control strategies rely on molecular genetic and genomic techniques — from elucidating the chemosensory cues that guide mosquitoes to blood-feed on their hosts, identifying and characterizing the molecular targets of insect repellents and insecticides, and developing genetically modified mosquitoes, including transgenic lines that produce sterile males or CRISPR-Cas9 based gene drives. The genome of Ae. aegypti is estimated to be 1.2-1.3 Gbp and has proven challenging to assemble in part because of high levels of repeat content and heterozygosity. The existing draft reference genome of Ae. aegypti, originally produced in 2007, is incomplete and highly fragmented. Prompted by the Zika crisis, we organized a collaborative effort to re-sequence and re-assemble this genome. As the foundation to this goal, a high-quality de novo genome assembly was produced by Pacific Biosciences using single molecule, real-time (SMRT) sequencing. This assembly achieved an order of magnitude improvement on the genome contiguity compared to the 2007 reference. The AGWG has also collected additional data from scaffolding technologies including optical map data from BioNano, ‘Chicago’ libraries from Dovetail Genomics Hi-C, and libraries generated using the 10X Genomics ‘Chromium’ platform. The goal of the AGWG is to integrate all these data types to generate a highly contiguous and essentially complete Ae. aegypti reference genome assembly vital for efforts to combat mosquito-borne diseases.