Haploid-resolved genome assemblies for the arboviral vectors Aedes aegypti and Aedes mascarensis

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Haploid-resolved genome assemblies for the arboviral vectors Aedes aegypti and Aedes mascarensis Project Summary/Abstract Aedes aegypti transmits several arboviral diseases including dengue and Zika fever, which threaten half of the human population worldwide. In this study, we will take advantage of Oxford Nanopore Technology (ONT) sequencing, the TrioCanu binning approach, and Hi-C scaffolding to create haploid-resolved chromosome- level genome assemblies for Ae. aegypti and Ae. mascarensis. These two closely related species show reproductive isolation by hybrid breakdown via formation of intersexes in backcross hybrids. The long-term objective of this research is to decipher the genetic mechanisms of reproductive isolation between Ae. aegypti and closely related species and to translate such fundamental knowledge into safe and efficient methods to control mosquito-borne infectious diseases. Understanding the permeability of species boundaries is increasingly urgent because of recent developments in transgenic- and gene drive-based applications to control disease vectors. The major goal of this proposed R21 project is to develop and validate phased or haplotype-resolved genome assemblies for Ae. aegypti and Ae. mascarensis and use them for identification and characterization of the genomic regions associated with intersex phenotypes in backcross hybrids between the two species. This timely project will meet the demand for new, highly-finished genome references for arboviral vectors based on appropriate innovative tools and the PI’s and Co-I’s expertise. Toward this goal, we propose the following three Specific Aims: (1) Obtain contiguous haploid genome assemblies for the Ae. aegypti RED strain and Ae. mascarensis by integrating ONT, Illumina sequencing, trio binning, and chromosome-scale Hi-C scaffolding; (2) Validate the obtained assemblies and construct high-resolution physical genome maps for Ae. aegypti and Ae. mascarensis using fluorescence in situ hybridization (FISH); and (3) Identify genomic regions in chromosome 1 that are associated with intersex phenotypes. The new, haploid-resolved chromosome-level genome assemblies for Ae. aegypti and Ae. mascarensis will be available to the scientific community through VEuPathDB and NCBI. Identification of the recombination breakpoints and characterization of genomic regions associated with intersex phenotypes will improve our understanding of the mechanisms that maintain species boundaries and determine sex in mosquitoes. The project will also help us to detect genome variations between these two species that may be important for speciation, adaptation, and vectoral capacity.