Release VB-2013-06
Overview
We are pleased to announce the June release of VectorBase (VB-2013-06). Highlights of this release include:
- Release of the VectorBase population biology (PopBio) resource.
- The Aedes aegypti gene set has been updated to version AaegL1.4
- Nine new Anopheles genome annotations have been added.
- The VectorBase Community Annotation Portal (CAP) is now accepting data for the nine Anophelines, Biomphalaria glabrata, Lutzomyia longipalpis, Phlebotomus papatasi.
- The VectorBase variation resource includes sequenced MR4 colony data from MalariaGEN.
- The genome browser has improved track documentation.
- The ontologies are updated, including new anatomy images for TGMA.
- VectorBase user accounts available for CAP, Forum and job histories (BLAST, ClustalW and HMMer).
- Better integration of BLAST into the new site has improved overall performance of this tool.
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.
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.
- BioMart.
- Browsing genomes: Visualizing and adding tracks.
- Using HMMER versus BLAST to find homologs.
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.
