Mosquitoes are vectors of numerous infectious diseases. To facilitate the development of advanced genome-based strategies for vector control, the genomes of the three major mosquito genera-Anopheles, Aedes, and Culex-were sequenced over the last decade. The genome assembly of Cx. quinquefasciatus, the major vector of the lymphatic filariasis worm and encephalitis viruses, is the most fragmented, with only 9% of the genome placed to the chromosomes. The lack of a high-quality, chromosome-based genome assembly for Cx. quinquefasciatus remains an impediment to further progress in Culex biology and comparative genomics of mosquitoes. Using the Next-Generation Focus Genome Sequencing (FGS) approach, recently developed by Amplicon Express, we will obtain ~250 Mb of high-quality sequence assemblies for 2304 BAC clones. Alignment of the sequences to the existing genome will greatly enhance the quality of the genome assembly. The total number of supercontigs will be reduced from 3171 to ~600. In addition, our project will develop a new cytogenetic map for Cx. quinquefasciatus based on mitotic chromosomes from imaginal discs of 4th instar larvae and anchor the majority of the genomic supercontigs to this map. The primary goal of this R21 proposal is to significantly improve the genome assembly for Cx. quinquefasciatus.
The specific aims for this project are to: 1) improve the quality of the genome assembly by sequencing 2304 BAC clones using Focus Genome Sequencing (FGS) and 2) create a chromosome-based genome assembly by multicolor fluorescent in situ hybridization (FISH) of ~1000 BAC clones to Cx. quinquefasciatus chromosomes. The availability of a high-quality genome assembly for Cx. quinquefasciatus will enhance research in vector biology. Results of this project will be disseminated through VectorBase.

Public Health Relevance

The southern house mosquito, Culex quinquefasciatus, is a principal vector of lymphatic filariasis worms and encephalitis viruses, including West Nile virus. The current genome assembly for this mosquito is highly fragmented, creating a major impediment to further progress in Culex biology and comparative genomics of mosquitoes. This project will significantly improve the genome assembly for this species through additional next-generation sequencing and extensive physical mapping.

National Institute of Health (NIH)
National Institute of Allergy and Infectious Diseases (NIAID)
Exploratory/Developmental Grants (R21)
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Vector Biology Study Section (VB)
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Costero, Adriana
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Virginia Polytechnic Institute and State University
Schools of Earth Sciences/Natur
United States
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Behura, S K (2015) Insect phylogenomics. Insect Mol Biol 24:403-11
Unger, Maria F; Sharakhova, Maria V; Harshbarger, Adam J et al. (2015) A standard cytogenetic map of Culex quinquefasciatus polytene chromosomes in application for fine-scale physical mapping. Parasit Vectors 8:307
Sharakhov, Igor V; Sharakhova, Maria V (2015) Heterochromatin, histone modifications, and nuclear architecture in disease vectors. Curr Opin Insect Sci 10:110-117
Behura, Susanta K; Severson, David W (2015) Motif mismatches in microsatellites: insights from genome-wide investigation among 20 insect species. DNA Res 22:29-38