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). Assembly of 8x shotgun coverage was performed using the Broad's whole genome assembly package ARACHNE. The assembly presented here (AaegL2, October 2009) consists of 4,758 supercontigs, totalling 1.3 gigabases. In release 22 of Ensembl Metazoa (March 2014) two bacterial contaminant scaffolds were removed, making the genome sequence consistent with the INSDC record.

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 (AaegL2.1, December 2013) represents the original set integrated with several rounds of community annotations, and the inclusion of additional gene predictions which were excluded from the AaegL1.1 set but subsequently found to have supporting evidence (transcriptome, mapped protein domains).

EST and Protein Alignments

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

WU-BlastX was used to map UniProtKB proteins onto the Aedes aegypti genome. The datasets used were: Aedes, mosquito, drosophilid, arthropod, metazoan, eukaryotic, and non-eukaryotic proteins. The wider taxonomic groups exclude any of the more specific groups, e.g. the arthropod dataset excludes mosquito and drosophilid proteins. (Example: supercont1.174:147000-580000).

Approximately 1300 community annotations are mapped to the genome (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.

Statistics

Summary

Assembly: AaegL2, INSDC Assembly GCA_000004015.1, Dec 2013
Database version: 75.2
Base Pairs: 1,310,090,344
Golden Path Length: 1,383,957,531
Genebuild method: Full genebuild
Table of top 500 InterPro hits

Gene counts

Coding genes

Genes and/or transcript that contains an open reading frame (ORF).

:
15,784
Short non coding genes

Short non coding genes are usually fewer than 200 bases long. They may be transcribed but are not translated. In Ensembl, genes with the following biotypes are classed as short non coding genes: miRNA, miscRNA, rRNA, tRNA, ncRNA, scRNA, snlRNA, snoRNA, snRNA, tRNA, and also the pseudogenic form of these biotypes. The majority of the short non coding genes in Ensembl are annotated automatically by our ncRNA pipeline.

:
1,358
Pseudogenes

A pseudogene shares an evolutionary history with a functional protein-coding gene but it has been mutated through evolution to contain frameshift and/or stop codon(s) that disrupt the open reading frame.

:
19

Coordinate Systems

supercontig 4756 sequences
contig 36206 sequences