Abstract
The Aedes aegypti mosquito is a major vector for arboviruses including dengue, chikungunya and zika. Combating the spread of these viruses requires a more complete understanding of mosquito-virus interactions. Recent studies have implicated DNA derived from non-retroviral RNA viruses in insect immunity. To better define the role and origin of these elements, we generated a high-quality assembly of the Ae. aegypti-derived Aag2 cell line genome using single-molecule, real-time sequencing technology. The new assembly improves contiguity by one to two orders of magnitude with respect to previously released assemblies. This improved quality enables characterization of the collection of Endogenous Viral Elements (EVEs) in the mosquito genome, providing insight into their integration and role in mosquito immunity. Additionally, we find a distinct repertoire of EVEs present in the genomes of Ae. aegypti and Ae. albopictus, suggesting the intriguing possibility that differences in EVE composition may play a role in establishing vector competence.