Aedes aegypti (LVP_AGWG) Assembly and Gene Annotation
About Aedes aegypti
Aedes aegypti exists in at least two forms (considered either subspecies or separate species according to different authors), namely Ae. aegypti formosus (the original wild type found in Africa) and Ae. aegypti aegypti (the worldwide urban form). The yellow fever mosquito, Ae. aegypti aegypti, has a worldwide distribution in the tropics and subtropics where it is the main vector of both dengue and yellow fever viruses. It can also transmit chikungunya and Zika viruses.
Picture credit (public domain): James Gathany (CDC) 2006
The Aedes aegypti Liverpool AGWG (LVP_AGWG) strain was sequenced as part of the Aedes aegypti Genome Working Group (AGWG) effort to improve the existing Liverpool strain assembly. The LVP_AGWG strain was generated from 3 generations of single pair inbreeding from inbred sub-strain LVPIB12 (Virginia Tech) as detailed in the BioSample record https://www.ncbi.nlm.nih.gov/biosample/SAMN07177802.
DNA sequencing was performed upon a pool of 80 whole male pupae siblings.
The genome sequence was produced at Rockefeller University by the Aedes aegypti Genome Working Group (AGWG). PacBio reads were assembled by FALCON-Unzip, scaffolded by Hi-C, and gap-filling and polishing performed by PBJ and arrow. The assembly presented here (AaegL5.0 June 2017) is chromosome level, and consists of 2,310 scaffolds, totalling 1.278 Gigabases, with a contig N50 of 11.8 Mb and supercontig N50 size of 409.8 Mb.
The assembly effectively supercedes the AaegL3 assembly, and is the supported assembly for the EnsemblMetazoa. The previous assembly for the Aedes aegypti Liverpool (LVP) strain (AaegL3) is deprecated, but can be found on EnsemblMetazoa archive.
Community annotation patch build for April 2019
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|Assembly||AaegL5, INSDC Assembly GCA_002204515.1,|
|Golden Path Length||1,278,732,104|
|Genebuild method||Full genebuild|
|Non coding genes||4,704|
|Small non coding genes||913|
|Long non coding genes||3,791|