Culex pipiens Database

Data site retirement

On 9/30/15 the Broad's Institute Culex pipiens database and web site will be retired due to expiration of funding. For many years we have been pleased to work closely with the Culex pipiens research community to create and support this resource. Genomic data can still be accessed via VectorBase.

Project Information

The Culex pipiens quinquefasciatus JHB whole-genome sequencing project is a joint effort between the National Institute of Allergy and Infectious Diseases funded Microbial Sequencing Centers (MSC) at the Broad Institute and The J. Craig Venter Institute. Genome Annotation was carried out in collaboration with VectorBase.

The goals of this sequencing effort are:

  1. To produce and publicly release a whole-genome assembly of the Cx. P. quinquefasciatus genome representing 8X sequence coverage.
  2. Generate expressed sequence tags (ESTs) from cDNA libraries prepared from Culex and from Culex harboring distinct pathogens.
  3. Produce and release a high quality automated annotation of the sequence assembly.

In collaboration, these centers have produced 8X coverage of the Culex genome as paired-end sequence reads from shotgun libraries prepared with a range of vector types and insert sizes. Assembly of the genome was performed using the Broad's whole genome assembly package ARACHNE (Batzoglou et al., 2002 and Jaffe et al., 2003). The Culex genome will be annotated in a collaborative effort involving both MSCs and Vectorbase, an NIAID-funded bioinformatics resource center at the University of Notre Dame and Ensembl.

Peter W. Atkinson of the University of California Riverside provided the genomic DNA for the sequencing project; the white paper for this organism was submitted by Peter W. Atkinson and Frank H. Collins (University of Notre Dame).

This assembly has been submitted to NCBI under the project accession AAWU01000000.

What is Culex pipiens quinquefasciatus?

Culex species are important vectors of human pathogens in the United States and world-wide, including the aetiologic agents of West Nile encephalitis, Eastern equine encephalitis, Venezuelan equine encephalitis, Japanese encephalitis, St. Louis encephalitis, Ross River encephalitis, Murray Valley encephalitis, Rift valley fever, and lymphatic filariases. The most important of the Culex vectors are members of the Culex pipiens complex, a very closely related group of species or incipient species that originated in Africa but has spread by human activity to tropical and temperate climate zones on all continents but Antarctica. The complex consists primarily of two subspecies, Culex pipiens pipiens and Culex pipiens quinquefasciatus. They are taxonomically recognized as subspecies due to the fact that they normally occupy different distributions, pipiens occurring in the more northern and more southern temperate regions of the world and quinquefasciatus occurring primarily in tropical and warm temperate regions.

The genome sequence of a member of the Cx. pipiens complex is intended to greatly simplify the identification of mosquito genes required for pathogen transmission and facilitate the development of new strategies for combating and controlling disease. Furthermore, the Culex pipiens quinquefasciatus JHB whole-genome sequencing project complements ongoing work with Anopheles gambiae and Aedes aegypti, providing genome assemblies for each of these three important representative mosquito vectors of human pathogens. This allows for comprehensive comparisons between representatives of the three mosquito genera and provides essential information required to inform the evolutionary relationships among these species, advancing our understanding of mosquito genes involved in important phenomena.


  • Jaffe DB, Butler J, Gnerre S, Mauceli E, Lindblad-Toh K, Mesirov JP, Zody MC, Lander ES. 2003. Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res. Jan;13(1):91-6.
  • Batzoglou S, Jaffe DB, Stanley K, Butler J, Gnerre S, Mauceli E, Berger B, Mesirov JP, Lander ES. 2002. ARACHNE: a whole-genome shotgun assembler. Genome Res. 2002 Jan;12(1):177-89.