Aedes aegypti (Yellow fever mosquito, 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

Assembly

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.

Annotation

AaegL5.3

Community annotation patch build for June 2020

References

1. Comparative analysis of response to selection with three insecticides in the dengue mosquito Aedes aegypti using mRNA sequencing.
   David JP, Faucon F, Chandor-Proust A, Poupardin R, Riaz MA, Bonin A, Navratil V, Reynaud S. 2014. BMC Genomics. 15:174-189.
2. Effective population sizes of a major vector of human diseases, Aedes aegypti.
   Saarman NP, Gloria-Soria A, Anderson EC, Evans BR, Pless E, Cosme LV, Gonzalez-Acosta C, Kamgang B, Wesson DM, Powell JR. 2017. Evolutionary applications. 10(10):1031-1039.
3. Evolution of mosquito preference for humans linked to an odorant receptor.
   McBride CS, Baier F, Omondi AB, Spitzer SA, Lutomiah J, Sang R, Ignell R, Vosshall LB. 2014. Nature. 515(7526):222.
4. Origin of a High-Latitude Population of Aedes aegypti in Washington, DC.
   Gloria-Soria A, Lima A, Lovin DD, Cunningham JM, Severson DW, Powell JR. 2018. The American Society of Tropical Medicine and Hygiene. 98(2):445-452.
5. Proteomics informed by transcriptomics for characterising active transposable elements and genome annotation in Aedes aegypti.
   Maringer K, Yousuf A, Heesom KJ, Fan J, Lee D, Fernandez-Sesma A, Bessant C, Matthews DA, Davidson AD.. 2017. BMC Genomics. 18(1):101
6. The Diversity, Structure, and Function of Heritable Adaptive Immunity Sequences in the Aedes aegypti Genome.
   Whitfield ZJ, Dolan PT, Kunitomi M, Tassetto M, Seetin MG, Oh S, Heiner C, Paxinos E, Andino R. 2017. Current Biology. 27(22):3511-3519.
7. Genome sequence of Aedes aegypti, a major arbovirus vector.
   Nene V, Wortman JR, Lawson D, Haas B, Kodira C, Tu ZJ, Loftus B, Xi Z, Megy K, Grabherr M et al. 2007. Science. 316:1718-1723.
8. Probing functional polymorphisms in the dengue vector, Aedes aegypti.
   Bonizzoni M, Britton M, Marinotti O, Dunn WA, Fass J, James AA. 2013. BMC Genomics. 14:739.
9. A multipurpose, high-throughput single-nucleotide polymorphism chip for the dengue and yellow fever mosquito, Aedes aegypti.
   Evans BR, Gloria-Soria A, Hou L, McBride C, Bonizzoni M, Zhao H, Powell JR. 2015. G3 (Bethesda). 5:711-718.