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

> **NIH NIH R21** · VIRGINIA POLYTECHNIC INST AND ST UNIV · 2022 · $195,322

## Abstract

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.

## Key facts

- **NIH application ID:** 10495269
- **Project number:** 5R21AI166878-02
- **Recipient organization:** VIRGINIA POLYTECHNIC INST AND ST UNIV
- **Principal Investigator:** IGOR V SHARAKHOV
- **Activity code:** R21 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $195,322
- **Award type:** 5
- **Project period:** 2021-09-24 → 2025-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10495269

## Citation

> US National Institutes of Health, RePORTER application 10495269, Haploid-resolved genome assemblies for the arboviral vectors Aedes aegypti and Aedes mascarensis (5R21AI166878-02). Retrieved via AI Analytics 2026-05-24 from https://api.ai-analytics.org/grant/nih/10495269. Licensed CC0.

---

*[NIH grants dataset](/datasets/nih-grants) · CC0 1.0*