A chromosome-level genome assembly for the major African malaria vector Anopheles gambiae

The African malaria mosquito Anopheles gambiae, because of its epidemiological importance, was the first disease vector, with a genome sequenced in 2002. Since then the PEST strain assembly remains the only available chromosome-level genome reference for this major African malaria vector. Although this assembly has been the workhorse for functional and population genomic studies of malaria mosquitoes for almost two decades, it is now failing to deliver the highest possible quality of the analyses as it is staggeringly imperfect by the modern standards. The assembly has serious deficiencies such as a large portion of unmapped contigs, sequencing and physical gaps, incorrect order and orientation of some scaffolds, and the presence of haplotypes derived from the sister species An. coluzzii. Moreover, the PEST strain of An. gambiae is no longer available and the existing assembly cannot be validated or improved with additional sequencing. As a result, a complete annotation and an accurate functional characterization of the An. gambiae genome cannot be performed. Also, the lack of a reliable reference represents a major impediment to population genomics studies, especially to those dealing with structural genomic variations. For a long time, the high cost of sequencing and the sheer difficulty of genome assembly has made major improvements of the mosquito genome prohibitive. Novel long-read sequencing technologies and innovative scaffolding approaches now allow developing de novo chromosome-level genome assemblies of superior quality at a reasonable cost. Also, the availability of polytene chromosomes ensures high- resolution genome mapping in An. gambiae.

A new chromosome-level genome assembly for An. gambiae will transform research as it will allow the most complete functional annotation and the most detailed population analysis of malaria mosquitoes. The more complete assembly of heterochromatic sequences will improve our understanding of the genomic “dark matter” and will stimulate epigenomic studies of this disease vector. The scientific community will have free access to the new assembly from VEuPathDB and NCBI.

NIH project details

Enabling Technologies & Assays
Vector Control

Feb 2021 — Jan 2024

$435,912

United States