Release VB-2018-02
We are pleased to announce the February 2018 release of VectorBase (VB-2018-02):
- Updates to the gene sets for 11 species based on community annotation ( Anopheles albimanus, A. arabiensis, A. coluzzii, A. darlingi, A. dirus, A. funestus, A. gambiae, A. merus, A. quadriannulatus, Pediculus humanus, and Stomoxys calcitrans ).
- Variation data from the Anopheles gambiae Ag1000g consortium AR3 data release is now available via the genome browser or programmatically via the REST API. This data set contains 50 million variant calls from 765 individual mosquitoes, from 15 different locations in Africa as described in the article Genetic diversity of the African malaria vector Anopheles gambiae by the Anopheles gambiae 1000 genomes consortium.
- Whole genome alignments have been updated for Aedes aegypti LVPAGWG strain versus Anopheles gambiae and Culex quinquefasciatus, and for Anopheles atroparvus versus Anopheles gambiae.
- Variation effect predictions have been updated for A. arabiensis, A. funestus, A. gambiae, A. merus and A. quadriannulatus.
- Expression microarray probes have been updated for A. funestus and A. gambiae.
- A new Apollo instance for the Aedes aegypti LVPAGWG strain is now available for gene curation.
- PopBio map genotypes view is ready for general use - view geographic allele distributions for Kdr, Gste2, Ace1 and Rdl genes.
- Two years of Southern Nevada abundance data added to PopBio
- User interface (UI) improvements made to the PopBio map, views, and download options
- Updated PopBio landing page
- All non-default selections of the PopBio map now get captured by the ‘Share view’ button. Sharing the view now correctly replicates the screen.
- Added help and tooltips for export and Advanced Search queries.
- New practice exercises and answer key for the Search tutorial. New sample queries for PopBio map and PopBio Search; the former include samples, insecticide resistance, abundance and genotypes, and the latter include these same type of queries plus infection status and blood meal identification.
- The schedule for 2018 outreach activities is available, including meetings where VectorBase is hosting a booth or presenting a talk or poster. Registration is open for workshop and webinars. This page features a new (beta) outreach calendar.
Genomes
Released genomes, with gene predictions
Expression data
New experiments processed and added to the expression browser:
- Hytrosavirus infection (Kariithi et al., 2017) Musca domestica RNA-seq experiment
- Sex-biased gene expression in albimanus (Papa et al., 2017) Anopheles albimanus RNA-seq experiment
- Sex-biased expression in gambiae (Papa et al., 2017) Anopheles gambiae RNA-seq experiment
- Adult heads infected with Trypanosoma brucei (Awuoche et al., 2017) Glossina morsitans RNA-seq experiment
Population Biology/Insecticide Resistance
13 projects have been added:
- Insecticide resistance to permethrin and malathion and associated mechanisms in Aedes aegypti mosquitoes from St. Andrew Jamaica (VBP0000216: details, map, 5 collections, 50 samples, 40 phenotypes, 20 genotypes)
- Polymorphisms in voltage-gated sodium channel gene and susceptibility of Aedes albopictus to insecticides in three districts of northern West Bengal, India (VBP0000217: details, map, 7 collections, 26 samples, 30 phenotypes, 26 genotypes)
- Insecticide susceptibility status of invasive Aedes albopictus across dengue endemic districts of Odisha, India. (VBP0000218: details, map, 10 collections, 70 samples, 40 phenotypes, 66 genotypes)
- First evidence of resistance to pyrethroid insecticides in Italian Aedes albopictus populations after 26 years since invasion (VBP0000219: details, map, 11 collections, 57 samples, 41 phenotypes, 0 genotypes)
- Insecticide susceptibility of Aedes aegypti and Aedes albopictus in Central Africa (VBP0000220: details, map, 6 collections, 43 samples, 60 phenotypes, 0 genotypes)
- Composition of Anopheles mosquitoes, their blood-meal hosts, and Plasmodium falciparum infection rates in three islands with disparate bed net coverage in Lake Victoria, Kenya (VBP0000221: details, map, 11 collections, 11 samples, 132 phenotypes, 0 genotypes)
- Distribution and abundance of key vectors of Rift Valley fever and other arboviruses in two ecologically distinct counties in Kenya (VBP0000222: details, map, 14 collections, 280 samples, 0 phenotypes, 0 genotypes)
- Increasing insecticide resistance in Anopheles funestus and Anopheles arabiensis in Malawi, 2011–2015 (VBP0000223: details, map, 103 collections, 202 samples, 202 phenotypes, 0 genotypes)
- Preliminary survey on Anopheles species distribution in Botswana shows the presence of Anopheles gambiae and Anopheles funestus complexes (VBP0000224: details, map, 26 collections, 404 samples, 416 phenotypes, 0 genotypes)
- Mosquito surveillance in Southern Nevada, USA. 2016 (VBP0000213: details, map, 930 collections, 2751 samples, 5463 phenotypes, 0 genotypes)
- Mosquito surveillance in Southern Nevada, USA. 2015 (VBP0000214: details, map, 745 collections, 2272 samples, 4581 phenotypes, 0 genotypes)
- Mosquito surveillance in Southern Nevada, USA. 2014 (VBP0000215: details, map, 625 collections, 1905 samples, 3840 phenotypes, 0 genotypes)
- Knockdown Resistance (kdr) Mutations in Indian Anopheles stephensi (Diptera: Culicidae) Populations (VBP0000225: details, map, 9 collections, 9 samples, 8 phenotypes, 21 genotypes)
- Comparative analysis of response to selection with three insecticides in the dengue mosquito Aedes aegypti using mRNA sequencing. (VBP0000121: details, 0 collections, 4 samples, 0 phenotypes, 0 genotypes)
- A multipurpose high throughput SNP chip for the dengue and yellow fever mosquito, Aedes aegypti (VBP0000122: details, map, 160 collections, 160 samples, 0 phenotypes, 0 genotypes)
- Probing functional polymorphisms in the dengue vector, Aedes aegypti (VBP0000015: details, 0 collections, 3 samples, 0 phenotypes, 0 genotypes)
- UC Davis/UCLA population dataset (VBP0000005: details, map, 819 collections, 30769 samples, 0 phenotypes, 198812 genotypes)
- Identifying genomic changes associated with insecticide resistance in the dengue mosquito Aedes aegypti by deep targeted sequencing (VBP0000125: details, 8 collections, 14 samples, 0 phenotypes, 0 genotypes)
- Multiple introductions of the dengue vector, Aedes aegypti, into California (VBP0000177: details, map, 16 collections, 519 samples, 0 phenotypes, 11015 genotypes)
- Effective population sizes of a major vector of human diseases, Aedes aegypti (VBP0000193: details, map, 29 collections, 1383 samples, 0 phenotypes, 30018 genotypes)
- Origin of a High-Latitude Population of Aedes aegypti in Washington, DC (VBP0000201: details, map, 7 collections, 292 samples, 0 phenotypes, 6952 genotypes)
- Insecticide-Treated Nets and Protection against InsecticideResistant Malaria Vectors in Western Kenya (VBP0000192: details, map, 97 collections, 97 samples, 97 phenotypes, 0 genotypes)
- Multiple mechanisms of resistance to pyrethroids in Anopheles gambiae s.l populations in Niger (VBP0000196: details, map, 7 collections, 63 samples, 52 phenotypes, 14 genotypes)
- Insecticide resistance status of malaria vectors in Lao PDR (VBP0000210: details, map, 133 collections, 250 samples, 285 phenotypes, 84 genotypes)
- Natural diversity of the malaria vector Anopheles gambiae (VBP0000163: details, map, 765 collections, 765 samples, 0 phenotypes, 7650 genotypes)
- Genotyping and permethrin-resistance phenotyping of Anopheles gambiae M and S form mosquitoes from Cameroon, Ghana, Uganda and Guinea-Bissau (VBP0000004: details, map, 4 collections, 1833 samples, 2 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 | 0.29 | 0.004 | 2017-12 | 2017-12 |
| Anopheles arabiensis | 10.2 | 0.98 | 2014-10 | 2018-02 |
| Anopheles culicifacies | 9.15 | 0.88 | 2014-10 | 2017-12 |
| Anopheles epiroticus | 3.28 | 0.25 | 2014-10 | 2017-12 |
| Anopheles farauti | 6.5 | 0.75 | 2015-06 | 2017-12 |
| Anopheles funestus | 12.9 | 0.47 | 2014-10 | 2018-02 |
| Anopheles gambiae | 51.2 | 14.9 | 2018-02 | 2018-02 |
| Anopheles melas | 3.7 | 0.41 | 2015-06 | 2017-12 |
| Anopheles merus | 6.1 | 0.53 | 2015-06 | 2018-02 |
| Anopheles minimus | 4.21 | 0.22 | 2014-10 | 2017-12 |
| Anopheles quadriannulatus | 10.1 | 0.89 | 2014-10 | 2018-02 |
| Anopheles sinensis | 5.84 | 0.41 | 2015-06 | 2017-12 |
| Anopheles stephensi SDA-500 | 5.8 | 0.57 | 2014-10 | 2017-12 |
| Anopheles stephensi Indian | 0.37 | 2014-10 | 2017-12 | |
| Ixodes scapularis | 1.78 | 2015-02 | 2017-12 |
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-2018-04) is scheduled for late April.
Other known issues
- The latest assembly for Anopheles atroparvus has not yet been loaded for the Apollo editor. A notification will be sent to registered Apollo users when the update has been completed (currently extimate - July 13th 2018).
Please report any problems to the helpdesk.
Release date:
Wednesday, February 21, 2018
