Release VB-2017-02
We are pleased to announce the February 2017 release of VectorBase (VB-2017-02):
- Updates to all species for RNA gene sets using alignment to Rfam (release 12.1) covariance models, and predictions from miRBase (release 21) and tRNAscan-SE. (Further details)
- Microarray probe mappings and variant effects have been updated for all species in light of the RNA gene model changes in this release
- The xref entries for gene symbols are now only attached to genes, and are no longer attached to transcripts
- New RNAseq track hub data has been added for the following species
- Aedes aegypti (+4 track hubs)
- Anopheles gambiae (+3)
- Anopheles stephensi (+1)
- Musca domestica (+1)
- Sarcoptes scabiei (+1, new)
- Phlebotomus papatasi (SRA version replacement)
Please note that as stated in the August 2016 (2016-08) VectorBase release notes the old style RNAseq search interface has been retired, and all RNAseq search functionality has now been incorporated into the standard site search facility. RNAseq alignments are now derived from the HISAT pipeline, and the old alignments generated by other methods have been retired.
- Four new RNA-seq differential expression experiments added to the expression browser
- Ten new population biology datasets added (and eight updated to improve data consistency)
- The Web Apollo annotation tool has been upgraded to v2.0.5
- The Galaxy tool has been upgraded to v16.10
- Multiple minor updates have been made to the VectorBase search interface.
- Download limits removed for logged in users. If you want an account, please contact us.
- New Web Apollo tutorial and PopBio video tutorial
- New pages with information about VectorBase standard (in-person) and webinar workshops.
Genomes
Released genomes, with gene predictions
Expression data
Links within the expression browser to experiment pages have now been shortened and simplified. This should make it more convenient to send URLs to colleagues. The experiments listed below are using the new shorter links.
New experiments processed and added to the expression browser:
- Anopheles stephensi male vs female (Jiang et al., 2015) Anopheles stephensi RNA-seq experiment
- Embryonic development (Hall et al., 2015) Aedes aegypti RNA-seq experiment
- Aedes aegypti male vs female (Jiang et al., 2015) Aedes aegypti RNA-seq experiment
- Larval midgut response to Cry11Aa toxin (Canton et al., 2015) Aedes aegypti RNA-seq experiment
Population Biology/Insecticide Resistance
10 projects have been added:
- Species composition and insecticide resistance status of Anopheles gambiae (s.l.) (Culicidae) in Kome, southern Chad and the implications for malaria control (6 samples, 6 collections, 17 phenotypes, 0 genotypes)
- Underestimation of foraging behaviour by standard field methods in malaria vector mosquitoes in southern Africa (6 samples, 6 collections, 5 phenotypes, 0 genotypes)
- Natural human Plasmodium infections in major Anopheles mosquitoes in western Thailand (91 samples, 81 collections, 66 phenotypes, 0 genotypes)
- Exposure to deltamethrin affects development of Plasmodium falciparum inside wild pyrethroid resistant Anopheles gambiae s.s. mosquitoes in Uganda (4 samples, 1 collections, 2 phenotypes, 5 genotypes)
- Composition and genetics of malaria vector populations in the Central African Republic (37 samples, 15 collections, 140 phenotypes, 0 genotypes)
- Insecticide susceptibility of Anopheles stephensi to DDT and current insecticides in an elimination area in Iran. (11 samples, 1 collections, 11 phenotypes, 0 genotypes)
- Discovery of Point Mutations in the Voltage-Gated Sodium Channel from African Aedes aegypti Populations: Potential Phylogenetic Reasons for Gene Introgression
(19 samples, 14 collections, 16 phenotypes, 20 genotypes) - Increasing the potential for malaria elimination by targeting zoophilic vectors (795 samples, 189 collections, 980 phenotypes, 0 genotypes)
- Insecticide susceptibility and vector status of natural populations of Anopheles arabiensis from Sudan (13 samples, 13 collections, 52 phenotypes, 0 genotypes)
- Patterns of insecticide resistance and knock down resistance (kdr) in malaria vectors An. arabiensis, An. coluzzii and An. gambiae from sympatric areas in Senegal (60 samples, 20 collections, 0 phenotypes, 57 genotypes)
8 projects have been updated (usually to fix minor data inconsistencies):
- Global Genetic Diversity of Aedes aegypti (3708 samples, 83 collections, 0 phenotypes, 88274 genotypes)
- Knockdown resistance (kdr) mutations in
Indian Anopheles culicifacies populations (9 samples, 9 collections, 2 phenotypes, 27 genotypes) - Multiple Insecticide Resistance in the Malaria Vector Anopheles funestus from Northern Cameroon Is Mediated by Metabolic Resistance Alongside Potential Target Site Insensitivity Mutations (10 samples, 10 collections, 28 phenotypes, 18 genotypes)
- Relationship between insecticide resistance and kdr mutations in the dengue vector Aedes aegypti in Southern China (5 samples, 5 collections, 10 phenotypes, 45 genotypes)
- Insecticide susceptibility of natural populations of Anopheles coluzzii and Anopheles gambiae (sensu stricto) from Okyereko irrigation site, Ghana, West Africa (3 samples, 3 collections, 7 phenotypes, 4 genotypes)
- Pyrethroid resistance and susceptibility to Plasmodium falciparum infection of Anopheles
coluzzii populations from Yaoundé (Cameroon) (7 samples, 7 collections, 7 phenotypes, 0 genotypes) - Spatial and Temporal Trends in Insecticide Resistance among Malaria Vectors in Chad Highlight the Importance of Continual Monitoring (42 samples, 33 collections, 130 phenotypes, 10 genotypes)
- Insecticide resistance status of Aedes aegypti in 10 localities in Colombia (20 samples, 10 collections, 119 phenotypes, 0 genotypes)
Variation Data
Summary of available variation data by organism
| Reference species | SNP calls (million) | Indel calls (million) | Last dataset update | Last variation effect update |
|---|---|---|---|---|
| Aedes aegypti | 0.33 | 0.004 | 2016-02 | 2017-02 |
| Anopheles arabiensis | 10.2 | 0.98 | 2014-10 | 2017-02 |
| Anopheles culicifacies | 9.15 | 0.88 | 2014-10 | 2017-02 |
| Anopheles epiroticus | 3.28 | 0.25 | 2014-10 | 2017-02 |
| Anopheles farauti | 6.5 | 0.75 | 2015-06 | 2017-02 |
| Anopheles funestus | 12.9 | 0.47 | 2014-10 | 2017-02 |
| Anopheles gambiae | 7.3 | 1.3 | 2016-02 | 2017-02 |
| Anopheles melas | 3.7 | 0.41 | 2015-06 | 2017-02 |
| Anopheles merus | 6.1 | 0.53 | 2015-06 | 2017-02 |
| Anopheles minimus | 4.21 | 0.22 | 2014-10 | 2017-02 |
| Anopheles quadriannulatus | 10.1 | 0.89 | 2014-10 | 2017-02 |
| Anopheles sinensis | 5.84 | 0.41 | 2015-06 | 2017-02 |
| Anopheles stephensi SDA-500 | 5.8 | 0.57 | 2014-10 | 2017-02 |
| Anopheles stephensi Indian | 0.37 | 2014-10 | 2017-02 | |
| Ixodes scapularis | 1.78 | 2015-02 | 2017-02 |
Tutorials
Follow this link for all the site tutorials, which includes material such as videos with its slides, practice exercises with answer keys, and sample files. Visit our new YouTube Channel to watch all our video tutorials, we plan to add one for each release. The video slides (including demo outlines), are in our regular tutorial pages. The new and updated tutorials for this release are:
Future releases
The next VectorBase release (VB-2017-04) is scheduled for late April.
Other known issues
Please report any problems to the helpdesk.
Release date:
Tuesday, February 21, 2017
