Release VB-2015-04
We are pleased to announce the April release of VectorBase (VB-2015-04):
- Several new changes and updates have been incorporated and can be visualized using the Genome Browser including:
- New variation datasets for Aedes aegypti
- Pairwise alignments for all Glossina species and Musca domestica created, viewable through the 'Comparative Genomics' section in the Genome Browser, and summarized at https://www.vectorbase.org/compara_analyses.html. As shown in the following two links/examples, to check the updates in your gene of interest go to the gene page, and in the gene or location tabs click on "Comparative Genomics" under the left hand side menu
- Community gene model updates added for Biomphalaria glabrata
- Projected gene descriptions added for Anopheles and Glossina species
- Protein features reannotated in all species. To check the updates in your gene of interest go to the gene page, click on the transcript tab and under the left hand side menu go to "Protein Information/Domanis & Features", as shown in this example
- Improved Trinity RNASeq alignments added for Glossina brevipalpis, G. fuscipes and G. palidipes in the "Trinity-assembled transcripts" track in the "RNAseq alignments" category of the Genome Browser
- Community annotation cross references updateds for all species. To check the updates in your gene of interest go to the gene page and under the left hand side menu click on "External References", as shown in this example
- Three microarray experiments relating to the reproductive tract of Anopheles gambiae mosquitoes have been added to the Expression Browser
- Beta release of new search facility for scaffold or supercontig identifiers. Give it a try using the Search box and the identifier supercont1.190 - Feedback welcome
- Made minor updates to the VectorBase content management system, search system and tools
- New documentation for both the Web Apollo and the Expression (microarray and RNAseq) tutorials
Genomes
VectorBase is committed to a new release every two months with all data freely available for public use based on NIH/NIAID policy. A list of these changes and the state of current versions on this date (e.g., current gene sets) can be found on the Releases section of VectorBase.
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 |
|---|---|---|---|---|---|
| Lutzomyia longipalpis | Jacobina | LlonJ1 | LlonJ1.1 | 10 429 | |
| Phlebotomus papatasi | Israel | PpapI1 | PpapI1.1 | 12 678 | |
In this release gene descriptions were projected from well-annotated species to other (reasonably closely-related) species, based on orthologies derived from VectorBase gene trees. For a description to be projected, a pair of orthologs must have >30% amino acid sequence identity and >66% sequence coverage. The species and gene ID from which a description is projected is included in the text of the new description. Descriptions were projected from 1) Anopheles gambiae to the other Anophelines; 2) Glossina morsitans to the other Glossinidae + Musca domestica; 3) Drosophila melanogaster to the Glossinidae + M. domestica.
Expression Data
The three new experiments are
- Female lower reproductive tract post-mating time-series (Gabrieli et at., 2014)
- Female lower reproductive tract 20E injection (Gabrieli et al., 2014)
- Mated vs virgin spermatheca (Shaw et al., 2014)
We have not regenerated the Anopheles gambiae cell-line only expression map for this release, but will do so in future release as required.
Population Biology/Insecticide Resistance
The population browser now contains metadata for 160 Aedes aegypti mosquitoes whose SNP chip-derived genotypes are available in the genome browser.
Variation Data
New data
New variation data added for Aedes aegypti form the paper "A multipurpose high throughput SNP chip for the dengue and yellow fever mosquito, Aedes aegypti"
Updates
Summary of available variation data by organism
| Reference species | SNP calls (million) | Indel calls (million) | Last updated |
|---|---|---|---|
| Aedes aegypti | 0.31 | 0.004 | 2015-04 |
| Anopheles arabiensis | 10.2 | 0.98 | 2014-10 |
| Anopheles culicifacies | 9.15 | 0.88 | 2014-10 |
| Anopheles epiroticus | 3.28 | 0.25 | 2014-10 |
| Anopheles funestus | 12.9 | 0.47 | 2014-10 |
| Anopheles gambiae | 7.3 | 1.3 | 2014-10 |
| Anopheles minimus | 4.21 | 0.22 | 2014-10 |
| Anopheles quadriannulatus | 10.1 | 0.89 | 2014-10 |
| Anopheles stephensi SDA-500 | 5.8 | 0.57 | 2014-10 |
| Anopheles stephensi Indian | 0.37 | 2014-10 | |
| Ixodes scapularis | 1.78 | 2015-02 |
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 | 2014-08 |
| Anopheles | Anopheles gambiae | Anopheline mitochondrial genes | 2014-08 |
| Culex | Culex quinquefasciatus | Culicine mitochondrial genes | 2014-08 |
| Ixodidae and Argasidae | Ixodes scapularis | Ixodida mitochondrial genes | 2014-08 |
Tutorials
Follow this link for the tutorials page, which also includes videos, practice exercises, and sample files. In this release these are the updates:
- Web Apollo: New features include a list of access points of interest for the ~50 min general video overview and a new video clip (of ~ 2:45 min) titled "Merging models and setting intron/exon boundaries".
- Expression (microarray and RNAseq): The tutorial slides have been updated to reflect the incorporation of RNAseq data and new display features.
Known issues
Please report any problems to the helpdesk.
