Aedes aegypti Assembly and Gene Annotation

VectorBase The Aedes aegypti data and its display on Ensembl Genomes are made possible through a joint effort by the Ensembl Genomes group and VectorBase, a NIAID Bioinformatics Resource Center. The source data for this genome and other resources can be accessed via the VectorBase browser.

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.

Picture credit (public domain): James Gathany (CDC) 2006

Assembly

The Aedes aegypti Liverpool LVP strain genome sequence is a joint effort between the Broad Institute and The Institute for Genomic Research (TIGR) [1]. Assembly of 8x shotgun coverage was performed using the Broad's whole genome assembly package ARACHNE. The assembly presented here (AaegL3) consists of 4,756 supercontigs and a mitochondrial chromosome, totalling 1.3 gigabases.

Annotation

The initial annotation of the Aedes aegypti genome is a collaboration between VectorBase and TIGR. Each group generated a set of gene predictions which were merged into a single canonical set (AaegL1.1). The geneset presented here (AaegL3.3, August 2014) represents the original set integrated with several rounds of community annotations; additional gene predictions that were excluded from the AaegL1.1 set but subsequently found to have supporting evidence (transcriptome, mapped protein domains); mitochondrial genes; and non-coding RNA genes from the Ensembl Genomes pipeline.

Variation

Two sets of variation data are available for Aedes aegypti, both imported via VectorBase.

The first is derived from the Bonizzoni et al. study [2]. This study used RNA-seq to characterise sequence variation in three laboratory strains of Aedes aegypti. An analysis of the transcriptomes from the Liverpool (LVP) reference strain, and two strains that exhibit differential susceptibility to Dengue-2 infection (Chetumal and Rexville D-Puerto Rico) was conducted, identifying many novel transcriptional units and polymorphisms in immunity related genes.

The second set of variation data covers multiple populations of Aedes aegypti, and was produced using a SNP chip containing 25K validated SNPs. This chip has been used to genotype a total of 160 individual insects from 25 Aedes aegypti populations isolated from 12 different regions around the world [3].

EST and Protein Alignments

Aedes aegypti ESTs were mapped onto the genome using Exonerate (Example: supercont1.174:147000-580000).

Proteins from all VectorBase species were mapped to the Aedes aegypti genome (using blastx) (Example: supercont1.174:147000-580000).

References

  1. 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.
  2. 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.
  3. 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.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyAaegL3, INSDC Assembly GCA_000004015.1, Dec 2013
Database version85.3
Base Pairs1,310,092,987
Golden Path Length1,383,974,186
Genebuild byVectorBase
Genebuild methodFull genebuild
Data sourceVectorBase

Gene counts

Coding genes15,796
Non coding genes1,663
Small non coding genes1,476
Long non coding genes3
Misc non coding genes184
Pseudogenes19
Gene transcripts18,840

Other

Short Variants310,480

About this species