Release VB_2012-06

Note, this is legacy information that refers to an older version of the VectorBase website.
Hyperlinks have been removed and URLs may no longer be valid.

Overview

Highlights of the June release of VectorBase (VB-2012-06) include:

  • New genomes: Anopheles darlingi and stephensi
  • New expression data for Anopheles gambiae and Aedes aegypti
  • Updated Anopheles albimanus transcriptome
  • Updated external references fixing known issues with April 2012 VectorBase release

Genomes

VectorBase is please to release two pre-sites for Phlebotomus papatasi and Lutzomyia longipalpis. Both of these have been released in GenBank and details can be found below.

Fully released genomes, with gene predictions

Species Assembly Gene set GenBank WGS
Aedes aegypti Liverpool AaegL1 AaegL1.3 AAGE02000000
Anopheles gambiae PEST AgamP3 AgamP3.7 AAAB01000000
Culex quinquefasciatus JHB CpipJ1 CpipJ1.3 AAWU01000000
Ixodes scapularis Wikel IscaW1 IscaW1.2 ABJB01000000
Pediculus humanus USDA PhumU1 PhumU1.2 AAZO01000000

Pre-released genomes, with mapped data but no gene predictions

Species Assembly GenBank WGS Data available
Anopheles gambiae M AgamM1 ABKP00000000 Repeats, ESTs
Anopheles gambiae S AgamS1 ABKQ00000000 Repeats, ESTs
Rhodnius prolixus CDC RproC1 ACPB00000000 Repeats, ESTs, RNA-seq and protein similarities - GenScan ab initio predictions and EST-build genes.
Glossina morsitans Yale GmorY1 - Repeats, RNA-seq (via BAM files) - EST-build genes, SNAP ab initio predictions, MAKER gene predictions.
Anopheles darlingi Adar11 ADMH00000000 Repeats, ENA and UniProtKB annotation.
Anopheles stephensi Indian Wild Type AsteV1 - Repeats, EST-build genes, SNAP ab initio predictions, MAKER gene predictions.

Expression Data

Data from three publications has been added as four experiments to the VectorBase Expression Browser, Expression BioMart, and Expression Maps:

  • Anopheles gambiae Plasmodium falciparum infections
  • Anopheles gambiae Plasmodium berghei infections
  • Sex-biased expression in larvae, pupae and adults
  • Aedes aegypti strain comparison, Bti larval pathogen resistance

Mitochondrial gene summaries for VectorBase genera

Links to Mitochondrial data for the 4 main genera are presented below for convenience.

Genus/genera Reference species Mitochondrial gene resource Last updated
Aedes Aedes aegypti http://aaegypti.vectorbase.org/SequenceData/Mitochondria/ 2012-06-03
Anopheles Anopheles gambiae http://agambiae.vectorbase.org/SequenceData/Mitochondria/ 2012-06-03
Culex Culex quinquefasciatus http://cquinquefasciatus.vectorbase.org/SequenceData/Mitochondria/ 2012-06-03
Ixodidae and Argasidae Ixodes scapularis http://iscapularis.vectorbase.org/SequenceData/Mitochondria/ 2012-06-03

Ontologies

VectorBase supports four ontologies developed by IMBB with members of the research community. These are available for browsing and download.

Ontology Version Description
MIRO 2.0 An ontology to describe mosquito populations, methods and mechanisms that are used to identify/monitor insecticide resistance.
TGMA 1.10 An ontology to describe the anatomy of mosquitoes.
TADS 1.21 An ontology to describe the anatomy of ticks.
IDOMAL 1.2.4 An ontology to describe all aspects of malaria. Clinical data, epidemiological data, biological data concerning vertebrate hosts, vectors and parasites as well as interventions and attempts to control the disease.

Ontology browser

The Controlled Vocabulary/Ontology browser has been upgraded. Most noteworthy changes:

  • it is now possible to search for terms using synonyms
  • term synonyms are now listed along with the rest of the term's details
  • OBO flat files can be downloaded by using the links on the main page of the CV browser

Known issues

VectorBase style stable identifiers have been produced for genes, transcripts and peptides for Anopheles darlingi when the original ENA identifiers should have been used. This will be changed in the next release.

Biomart has not yet been updated with the new genomes; we anticpate this being released within a week

Please report any problems to the helpdesk.

Release date: 
Saturday, June 30, 2012