Release VB-2013-06

Overview

We are pleased to announce the June release of VectorBase (VB-2013-06). Highlights of this release include:

Genomes

Released genomes, with gene predictions

Species Assembly Gene set GenBank WGS
Aedes aegypti Liverpool AaegL1 AaegL1.4 AAGE02000000
Anopheles darlingi Coari AdarC1 AdarC1.1 ADMH00000000
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
Rhodnius prolixus CDC RproC1 RproC1.1 ACPB00000000
Glossina morsitans Yale GmorY1 GmorY1.1  

Pre-released genomes, with mapped data and gene predictions

Species Assembly Gene set GenBank WGS
Anopheles albimanus STECLA AalbSI1 AaIbS1.0 APCK01000000
Anopheles arabiensis Dongola AaraD1 AaraD1.0 APCN01000000
Anopheles christyi ACHKN1017 AchrA1 AchrA1.0 APCM01000000
Anopheles dirus WRAIR2 AdirW1 AdirW1.0 APCL01000000
Anopheles epiroticus Epiroticus2 AepiE1 AepiE1.0 APCJ01000000
Anopheles funestus FUMOZ AfunF1 AfunF1.0 APCI01000000
Anopheles minimus MINIMUS1 AminM1 AminM1.0 APHL01000000
Anopheles quadriannulatus SANGWE AquaS1 AquaS1.0 APCH01000000
Anopheles stephensi SDA-500 AsteS1 AsteS1.0 APCG01000000
Anopheles stephensi Indian Wild Type AsteI1 AsteI1.0  
Lutzomyia longipalpis Jacobina LlonJ1 LlonJ1.0 AJWK01000000
Phlebotomus papatasi Israel PpapI1 PpapI1.0 AJVK01000000
Biomphalaria glabrata BB02 BglaB1 BglaB1.0  

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

Genome annotation

Manual annotations of the Ae. aegypti genome have been used for a gene set update. The AaegL1.4 geneset contains 17,391 genes with 393 modifications and 45 novel predictions added. The history of the gene identifiers is tracked within the search indices and alignments of the predicted sequences can be found in the 'Community annotation' track in the genome browser.

First-pass annotation using ab initio and similarity based approaches merged using Maker are available for the nine Anopheline genome assemblies available from the previous VectorBase release. The contig/scaffolds have been renamed in line with GenBank accessions and soft-masked sequences are available for download along with predicted transcript/peptide sequences. These genomes will now move into a community annotation phase.

Population Biology

The PopBio browser is now official and no longer in Beta testing. This resource provides information about population samples, assays performed on them (e.g. phenotyping, karyotyping, high-throughput genotyping), and the projects to which they belong. Samples from the MR4 colony resequencing project (see next item) link right through to variation data in the genome browser and vice-versa. The data submission process has been greatly simplified and we welcome your input.

Variation Data

The VB-2013-06 variation database release contains SNP and indel calls derived by sequencing of individual insects from the following MR4 Anopheles gambiae colonies.

  1. 4ARR
  2. KISUMU
  3. Akron
  4. L3-5
  5. G3

These samples were sequenced by the Wellcome Trust Sanger Institute, as part of the Malaria Programme's Anopheles gambiae Genome Variation Project. These variants have had limited quality filtering and should be considered preliminary.

Expression Data

No new experiments have been added.

Please note however that the expression resources have not been updated in line with the new Aedes aegypti gene set. This means that new or modified gene models may not currently have gene expression summaries or they may be based on out-dated microarray probe mappings.

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 Aedine mitochondrial genes 2013-06-11
Anopheles Anopheles gambiae Anopheline mitochondrial genes 2013-06-11
Culex Culex quinquefasciatus Culicine mitochondrial genes 2013-06-11
Ixodidae and Argasidae Ixodes scapularis Ixodida mitochondrial genes 2013-06-11

Ontologies

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

Ontology Version Description
GAZ 1.512 A controlled vocabulary of geographic locations.
GO 2013-04-02 The gene ontology.
IDODEN 0.3 Beta release of an an ontology that describes all aspects of Dengue. Clinical data, epidemiological data, biological data concerning vertebrate hosts, vectors and viruses as well as interventions and attempts to control the disease.
IDOMAL 1.2.9 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. This version includes a section describing natural therapies and remedies.
MIRO 2.1 An ontology to describe mosquito populations, methods and mechanisms that are used to identify/monitor insecticide resistance.
TADS 1.22 An ontology to describe the anatomy of ticks.
TGMA 1.12 An ontology to describe the anatomy of mosquitoes. This version contains all the images from the book "Anatomical drawings of the biting flies".

Tutorials

VectorBase held a workshop at the University of Notre Dame during the Arthropod Genomics Symposium (AGS) for nearly 60 participants. Please see below for attendee's most liked tutorials updated for the new site! If you have any questions or comments, please contact us at info@vectorbase.org.

Known issues

  • Aedes aegypti gene expression summaries are not up to date with the AaegL1.4 geneset. This means that new or modified gene models may not currently have gene expression summaries or they may be based on out-dated microarray probe mappings.

Please report any problems to the helpdesk.

Release date: 
Thursday, June 27, 2013