# A New Foundation for Leishmaniasis Vector Research and Control Through Generation of High-quality Sand Fly Genome Assemblies.

> **NIH NIH R03** · UNIVERSITY OF CALIFORNIA AT DAVIS · 2020 · $92,500

## Abstract

Project Summary
Leishmaniasis is the second biggest parasitic killer after malaria. It is estimated to kill an estimated 40,000 people
every year, and accounts for an estimated 2.4 million disability-adjusted life-years (DALYs). The Leishmania
parasite is transmitted to humans when female sand flies bite humans to obtain blood meals that they require
for reproduction. A better understanding of sand fly biology and populations is important for the control and
monitoring of this disease vector. This proposal will generate a high-quality genome references to support future
sand fly and Leishmania control efforts.
New and ongoing methods of integrated vector control are improved by genomic analysis. Descriptions of
species complexes, estimation of effective population sizes, monitoring of pesticide resistance allele emergence,
and assessment of changes in population structure can all be accomplished using genetic analyses. New vector
control methods based on CRISPR-Cas9 manipulation to create gene drives to prevent transmitting malaria and
microbiome manipulation with Wolbachia to prevent transmission of dengue are being trialed in mosquitoes.
Unfortunately, our early attempts to create high-quality genome reference resources for sand flies were not
successful. This study will generate new, very high-quality reference genome sequences for two critical sand fly
species: Lutzomyia longipalpis, found in the New World, is the primary vector of American visceral leishmaniasis
and Phlebotomus papatasi, found in the Old World, including northern Africa, the Middle East and India, is a
vector of cutaneous leishmaniasis.
New DNA sequencing and genome assembly techniques have improved the quality and reduced the cost to
generate new reference genomes. This study will generate multiple high-quality DNA sequence information
datasets for new high-quality genome assemblies. The primary sequence information will be long read (10-15
thousand bases) high accuracy (> 99.8%) DNA sequences using new DNA sequencing platforms from a single
individual of each species. HiC chromatin sequence data will be generated to understand the relative
chromosome position of the sequences. Optical mapping data will enable better scaffolding and validation of the
final assembly. A genome assembly software pipeline based on the vertebrate genome assembly pipeline
currently generating the highest quality reference genome assemblies will be used to assemble the data as much
as possible separating haplotypes. Long read high accuracy transcriptome data will be generated to support a
high-quality genome annotation, and the sand flies' microbiomes to fully characterize the environment of
Leishmania in these vectors. The final product will be a high-quality genome reference foundation for future
efforts to monitor and control the vector of this devastating disease.

## Key facts

- **NIH application ID:** 10043436
- **Project number:** 1R03AI153899-01
- **Recipient organization:** UNIVERSITY OF CALIFORNIA AT DAVIS
- **Principal Investigator:** MARY A MCDOWELL
- **Activity code:** R03 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2020
- **Award amount:** $92,500
- **Award type:** 1
- **Project period:** 2020-06-10 → 2021-05-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10043436

## Citation

> US National Institutes of Health, RePORTER application 10043436, A New Foundation for Leishmaniasis Vector Research and Control Through Generation of High-quality Sand Fly Genome Assemblies. (1R03AI153899-01). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10043436. Licensed CC0.

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