Release VB_2011-06
Hyperlinks have been removed and URLs may no longer be valid.
Overview
Highlights of the June release of VectorBase (VB-2011-06) include:
- Pre-site for Glossina moritans. Features mapped to the genome and preliminary gene sets available (see below).
- Glossina moritans assembly available for BLAST searching.
- New microarray data from Christian et al. and Cassone et al.
Genomes
The Glossina morsitans genome is available as pre-site: facilitates the browsing of the genome assembly with repeats and RNA-seq alignments, as well as EST-build genes, ab initio SNAP predictions and MAKER predictions.
Please note that these gene predictions are "work in progress" and will not be maintained as such in the final gene set. Full gene predictions will follow in a subsequent VectorBase release.
Fully released genomes, with gene predictions
| Species | Assembly | Gene set | GenBank WGS |
|---|---|---|---|
| Aedes aegypti Liverpool | AaegL1 | AaegL1.2 | AAGE02000000 |
| Anopheles gambiae PEST | AgamP3 | AgamP3.6 | AAAB01000000 |
| Culex quinquefasciatus JHB | CpipJ1 | CpipJ1.2 | AAWU01000000 |
| Ixodes scapularis Wikel | IscaW1 | IscaW1.1 | 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
Data from two recent publications have been added to the Expression Browser:
| Publication | Expression Browser link | Species | Description |
|---|---|---|---|
| Christian et al., Pesticide Biochemistry and Physiology Volume 99, Issue 2 | Anopheles funestus pyrethroid resistant vs. susceptible (Christian et al., 2010) | Anopheles funestus (using an Anopheles gambiae array) | Gene expression differences between a pyrethroid resistant strain (FUMOZ-R) of Anopheles funestus from Mozambique and a susceptible strain (FANG) of the same species from Angola were measured using the "Detox" chip designed for Anopheles gambiae, which features mostly detoxification genes. Adult females and males have been assayed separately. |
| Cassone et al., Mol Ecol. 2011 May 3 | Response to thermal stress in 2La and 2L+(a) karyotype mosquitoes (Cassone et al., 2011) | Anopheles gambiae | Anopheles gambiae larvae with or without the 2La chromosomal inversion were assayed for gene expression differences in the presence or absence of thermal stress at three time points. |
The resource now contains 42 experiments, assaying 120 experimental conditions over three species.
The Expression BioMart and (Anopheles gambiae) Expression Map have been updated with the new data. Note that the Expression Map analysis now excludes experimental conditions with fewer than 1000 assayed genes and genes with fewer than 10 assayed conditions.
As always, all microarray designs present in the Expression Browser are available as "Probe feature" tracks in the Genome Browser (they are not switched on by default, however).
Genome browser
The latest version (62) of the Ensembl genome browser software has been installed at VectorBase. This version features more informative and functional track labels (mouse-over to find out more) when in Location View.
Download data
New Glossina morsitans genome data is now available for download. Some naming confusions have been remedied throughout the downloads section.
Additionally, RNAseq transcriptome FASTA file downloads for nine Anopheline species have been made available via their annotation browser homepages which are linked from the newly re-vamped Additional Organisms page
Mitochondrial gene summaries for VectorBase genera
Mitochondrial sequences for genus Anopheles, genus Aedes, family Ixodidae, family Argasidase, genus Culex from GenBank (as of 2011-05-23) 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/ | 2011-05-23 |
| Anopheles | Anopheles gambiae | http://agambiae.vectorbase.org/SequenceData/Mitochondria/ | 2011-05-23 |
| Culex | Culex quinquefasciatus | http://cquinquefasciatus.vectorbase.org/SequenceData/Mitochondria/ | 2011-05-23 |
| Ixodidae and Argasidae | Ixodes scapularis | http://iscapularis.vectorbase.org/SequenceData/Mitochondria/ | 2011-05-23 |
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. |
Tools
Blast now includes new Glossina morsitans data.
Known issues
None at present.
Please report any problems to the helpdesk.
