||The Aedes aegypti Genome Project
We conducted an NIH NIAID funded project (UO1 AI050936) that has produced a complete annotated genome sequence for the yellow fever mosquito Aedes aegypti. Our initial intent for this project was to develop a body of genome information including EST sequences, genomic sequences, and the physical map positions of large genomic clones that will enhance gene discovery, and also provide critical front-end tools for the whole-genome sequencing effort. My collaborators were Dr. Dennis Knudson at Colorado State University, Drs. Brendan Lofus and Vish Nene at The Institute for Genome Research (TIGR), and Dr. Bento Soares at the University of Iowa.
BAC end sequences were obtained from 3 independently derived libraries and are publicly available in the GSS database at NCBI. A total of 117,937 sequences with an average read length of ~650 bp have been deposited: CC065891-CC144307, CC149837-CC155974, CC841856-CC875159. In addition, we have performed shotgun sequencing of 28 randomly selected BAC clones to assess genome suitability for cloning, sequencing and assembly. The individual assemblies are also available for download or online searches.
Normalized cDNA libraries were prepared from the Brugia malayi infected females, Plasmodium gallinaceum infected females, dengue-infected females,fatbody, and combined all life stages have been end sequenced. This effort generated about 211,000 sequences. These sequences can be accessed at the Aedes aegypti Gene Index AeGI that integrates data from this project with existing data in the EST and gene databases. Our EST sequences also have been deposited in the EST database at NCBI.
We received notification from NIH-NIAID on February 13, 2004 that our White Paper request to sequence the entire Aedes aegypti genome was approved. The whole genome shotgun sequencing effort was conducted conducted at TIGR and the Broad Institute. The genome assembly was released in October 2005 and has been deposited in GenBank under accession version AAGE02000000.
A preliminary v0.5 genome annotation was prepared jointly by TIGR and VectorBase. The TIGR release included 28,301 gene predictions, while the VectorBase release include 17,776 gene predictions. Both sets are available for genome view and BLAST analysis at VectorBase.
The final v1.0 genome annotation was released through GenBank on June 14, 2006 under the accession version AAGE00000000. The release contains 15,419 high confidence protein coding genes plus alternate spliced transcripts from 992 genes that add 1,370 proteins, for a total of 16,789 proteins. The annotated supercontigs are all available at GenBank and VectorBase. A simple search of the nucleotide database by supercontig number will find it; for example searching on supercont1.1 brings up accession CH477186. Other links to data for Aedes aegypti are available at the NCBI Genome Project site. In addition, a number of files containing a variety of data for the genome project are available for download at VectorBase.
Manual gene annotations by the Aedes aegypti research community are welcomed: please see Annotation Guidelines for submission instructions.
Details on the genome assembly and annotation were published in the June 22, 2007 issue of Science (316:1718-1722).
Our Plans for the Aedes aegypti genome project are described in the Project Plan.
The annotated Aedes aegypti genome sequence is displayed for public access and query at VectorBase.
Please feel free to contact me for further information.
Link to NIH CRISP Abstract
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