Release VB-2014-02
Overview
We are pleased to announce the February release of VectorBase (VB-2014-02):
- New ncRNA gene predictions for all species. This necessitates the incrementing of gene set versions across the board.
- First-pass annotation using MAKER of the Anopheles coluzzii genome, formerly Anopheles gambiae M molecular form
- Inclusion of second tranche of Anopheline genomes into compara and biomart
- Anopheline loci are highlighted with background colour in genetrees to make visualisation easier
- Minor usability improvements to BLAST.
- Added N50 for assembly information and it now is displayed on summaries.
- Update to the chromosomal divsions for An. gambiae PEST, data kindly supplied by Igor Sharakov
- Update to the BLAST and Advanced Search tutorials and, the update of some FAQs (click here and here for two examples).
- The latest issue of VectorBase Newsletter which includes information about VectorBase user group, a callout for pictures, the announcement of a new VectorBase workshop and more.
Genomes
VectorBase is committed to a new release every two months with all data freely available for public use based on NIH/NIAID policy.
For your species of interest, click on Organism, Strain, Assembly, or Gene set to find the Genome Browser link (which looks like this: 
).
Released genomes, with gene predictions
Pre-released genomes, with mapped data and gene predictions
| Organism | Strain | Assembly | Gene set | Gene Count | Browser |
|---|---|---|---|---|---|
| Anopheles coluzzii | Mali-NIH | AcolM1 | AcolM1.0 | 14 703 | |
| Biomphalaria glabrata | BB02 | BglaB1 | BglaB1.1 | 14 351 | |
| Lutzomyia longipalpis | Jacobina | LlonJ1 | LlonJ1.1 | 10 429 | |
| Phlebotomus papatasi | Israel | PpapI1 | PpapI1.1 | 12 678 | |
Pre-released genomes, with mapped data but no gene predictions
| Species | Assembly | GenBank WGS | Data available |
|---|---|---|---|
| Anopheles gambiae S | AgamS1 | ABKQ00000000 | Repeats, ESTs |
Genome annotation
The first-pass MAKER-based annotation of Anopheles coluzzii is available through the genome browser and Blast search/downloads. An. coluzzii is a new species previously regarded as a molecular form of An. gambiae and hence this gene set is built from the legacy Mali-NIH M-form assembly previously hosted at VectorBase.
Expression Data
No new data, but all expression resources have been rebuilt to incorporate minor updates to the AgamP3.8 and AaegL2.2 gene sets.
Population Biology/Insecticide Resistance
Added four new studies:
de Souza et al., Distribution of the Anopheles coluzzii and Anopheles gambiae s.s from Freetown and Monrovia and kdr resistance allele, West Africa
de Carvalho et al., Susceptibility of Aedes aegypti larvae to the insecticide temephos in the Federal District, Brazil.
Mekuria et al., Insecticide susceptibility of Aedes aegypti from Santo Domingo, Dominican Republic.
Brengues et al., Pyrethroid and DDT cross-resistance in Aedes aegypti is correlated with novel mutations in the voltage-gated sodium channel gene.
Corrected geographic coordinates in:
Kelly-Hope LA et al., Spatiotemporal distribution of insecticide resistance in Anopheles culicifacies and Anopheles subpictus in Sri Lanka.
In addition, several improvements have been made to the population biology browser's user interface: including info panels for clicked-on ontology terms and clickable markers on the Google maps.
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 | 2014-02 |
| Anopheles | Anopheles gambiae | Anopheline mitochondrial genes | 2014-02 |
| Culex | Culex quinquefasciatus | Culicine mitochondrial genes | 2014-02 |
| Ixodidae and Argasidae | Ixodes scapularis | Ixodida mitochondrial genes | 2014-02 |
Ontologies
| Ontology | Version | Description | Changes in this release |
|---|---|---|---|
| GAZ | 1.512 | A controlled vocabulary of geographic locations. | |
| GO | 2014-02-12 | The gene ontology. | Updated to 2014-02-12 daily release. |
| IDODEN | 0.15b | 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. | Structural changes to accommodate the addition of Dengue virus serotype 5. |
| IDOMAL | 1.36 | 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 adds a new approach on term linking, for example, role bearing entities will be defined as 'material entities' which bear the appropriate role. |
| 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. |
Tutorials
Follow this link for an updated version of the BLAST and Advanced search tutorials: https://www.vectorbase.org/tutorials
Known issues
Please report any problems to the helpdesk.
