Release VB_2011-10

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 October release of VectorBase (VB-2011-10) include:

  • Several major new microarray experiments added for Anopheles gambiae and Aedes aegypti.
  • Flat file expression downloads and an expression map are now available for Aedes aegypti.

Genomes

No new genomic data has been released or updated.

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 morsitansYale GmorY1 - Repeats, RNA-seq (via BAM files) - EST-build genes, SNAP ab initio predictions, MAKER gene predictions.

Expression data

Nine experiments have been added, from five publications:

Circadian rhythm in Anopheles gambiae, heads and bodies in two light regimes (Rund et al., 2011):

  • heads: dark-dark
  • heads: light-dark
  • bodies: dark-dark
  • bodies: light-dark

Adult tissues (Baker et al., 2011) - a.k.a. MozAtlas data (Anopheles gambiae)

Ageing in Anopheles gambiae:

  • Adult male mosquito ageing (Cook & Sinkins, 2010)
  • Adult female mosquito ageing (Cook & Sinkins, 2010)

Two Aedes aegypti insecticide/xenobiotic experiments:

  • Imidacloprid-resistant vs. susceptible larvae and adults (Riaz et al., 2011)
  • Xeniobiotic pre-exposed permethrin-resistant strains (Poupardin et al., 2011)

Legibility of the "x-axis" labels on the expression plots has been improved.

Expression maps

As usual, the Anopheles gambiae expression map has been updated with the new experimental data (now clustering 12k+ genes over 183 experimental conditions).

New for this release is the first Aedes aegypti expression map. It visualises the expression of 13k+ genes over 24 experimental conditions.

Genome browser

The probes for the microarray used in the two Aedes aegypti experiments listed above have been mapped to the genome and can be visualised in Location View by enabling the LIV_AGILENT_8X15K_V1 track.

Mitochondrial gene summaries for VectorBase genera

Mitochondrial sequences for genus Anopheles, genus Aedes, family Ixodidae, family Argasidase, genus Culex from GenBank (as of 2011-09-16) have been BLASTed against the corresponding reference mitochondrial genome, and the results have been grouped by matching genes.

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/ 2011-09-16
Anopheles Anopheles gambiae http://agambiae.vectorbase.org/SequenceData/Mitochondria/ 2011-09-16
Culex Culex quinquefasciatus http://cquinquefasciatus.vectorbase.org/SequenceData/Mitochondria/ 2011-09-16
Ixodidae and Argasidae Ixodes scapularis http://iscapularis.vectorbase.org/SequenceData/Mitochondria/ 2011-09-16

Ontologies

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

There are no updates for this release.

Ontology Version Description
MIRO 1.8 An ontology to describe mosquito populations, methods and mechanisms that are used to identify/monitor insecticide resistance.
TGMA 1.1 An ontology to describe the anatomy of mosquitoes.
TADS 1.2 An ontology to describe the anatomy of ticks.
IDOMAL 1.2 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.

Known issues

Alignments linked to through the "view raw alignment" drop-down in BLAST results may be significantly truncated. Please use the "view raw results" link for details on all alignments. We are working to resolve this issue in time for the next release.

Please report any problems to the helpdesk.

Release date: 
Monday, October 31, 2011