Release VB-2017-10
We are pleased to announce the October 2017 release of VectorBase (VB-2017-10):
- The PopBio map has an all-new abundance view mode which visualizes quantitative longitudinal collection data. It currently shows two years' of data from Iowa and two ICEMR studies from India. More to come!
- Permanent links to specific PopBio views are now available to enable easy sharing of your results with others
- In this release there were updates to the gene sets for 30 species based on community annotation ( Aedes aegypti, Anopheles albimanus, A. arabiensis, A. atroparvus, A. christyi, A. coluzzii, A. culicifacies, A. darlingi, A. dirus, A. epiroticus, A. farauti, A. funestus, A. gambiae, A. maculatus, A. melas, A. merus, A. minimus, A. quadriannulatus, A. sinensis, A. stephensi, Culex quinquefasciatus, Glossina austeni, Glossina brevipalpis, Glossina fuscipes, Glossina morsitans, Glossina pallidipes, Ixodes scapularis, Pediculus humanus, Rhodnius prolixus and Stomoxys calcitrans ).
- New variation data for Aedes aegypti has been added from the publications Effective population sizes of a major vector of human diseases, Aedes aegypti (Saarman et al, 2017) and Multiple introductions of the dengue vector, Aedes aegypti, into California. (Pless et al, 2017).
- SIFT predictions of whether an amino acid substitution affects protein function have been calculated for all species with variation data. Summary statistics for each species are shown in the Variation data section of the release notes as shown below.
- New RNAseq data have been added as track hubs in this release for Aedes aegypti, Anopheles albimanus, Anopheles arabiensis, Anopheles gambiae, Anopheles minimus, Anopheles sinensis and Musca domestica.
- Microarray probes are now displayed via trackhubs and can be searched for and displayed in same manner as other expression tracks (see the FAQ for expression array data for further information).
- INSDC accessions have been added for Glossina morsitans contig sequences, from the GCA_001077435.1 assembly.
- Differential expression data added, including for the bed bug
- Six new insecticide resistance studies
- Over 2,000 new genotyped Aedes aegypti samples have been added
- The BLAST tool now allows for Gene ID lookups through the input box. Please see Blast Tutorial for more details.
- We have updated 13 of our tutorials. These include new slides, practices exercises and answer keys. All VectorBase help and documentation materials have a Creative Commons Attribution-ShareAlike 4.0 International license. Enjoy!
Genomes
Released genomes, with gene predictions
Expression data
Four new experiments from three publications were processed and added to the expression browser:
- Pesisticide resistance in the bedbug (Mamidala et al., 2012) Cimex lectularius RNA-seq experiment
- Sex-biased gene expression in minimus (Papa et al., 2017) Anopheles minimus RNA-seq experiment
- Sex-biased gene expression in arabiensis (Papa et al., 2017) Anopheles arabiensis RNA-seq experiment
- Antennae and blood feeding (Chen et al., 2017) Anopheles sinensis RNA-seq experiment
Population Biology/Insecticide Resistance
Ten projects have been added:
- State-wide mosquito surveillance in Iowa, USA. 2013-2014 (VBP0000194: details, map, 7000 collections, 19175 samples, 2680 phenotypes, 0 genotypes)
- Insecticide resistance is mediated by multiple mechanisms in recently introduced Aedes aegypti from Madeira Island (Portugal) (VBP0000195: details, map, 16 collections, 16 samples, 8 phenotypes, 16 genotypes)
- Multiple mechanisms of resistance to pyrethroids in Anopheles gambiae s.l populations in Niger (VBP0000196: details, map, 7 collections, 63 samples, 52 phenotypes, 7 genotypes)
- Evaluation of piperonyl butoxide in enhancing the efcacy of pyrethroid insecticides against resistant Anopheles gambiae s.l. in Ghana (VBP0000197: details, map, 40 collections, 80 samples, 78 phenotypes, 0 genotypes)
- Habitat productivity and pyrethroid susceptibility status of Aedes aegypti mosquitoes in Dar es Salaam, Tanzania (VBP0000198: details, map, 6 collections, 144 samples, 144 phenotypes, 0 genotypes)
- Susceptibility to insecticides and resistance mechanisms in Aedes aegypti from the Colombian Caribbean Region. (VBP0000199: details, map, 9 collections, 81 samples, 81 phenotypes, 0 genotypes)
- Pyrethroid susceptibility of malaria vectors in four Districts of western Kenya (VBP0000200: details, map, 111 collections, 111 samples, 111 phenotypes, 0 genotypes)
- Tracking the return of Aedes aegypti to Brazil, the major vector of the dengue, chikungunya and Zika viruses (VBP0000176: details, map, 30 collections, 1032 samples, 0 phenotypes, 24566 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)
- 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)
- 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)
Variation Data
Summary of available variation data by organism
| Reference species | SNP calls (million) | Indel calls (million) | Last dataset update | Last variation effect update | mean SIFT per transcript |
|---|---|---|---|---|---|
| Aedes aegypti | 0.33 | 0.004 | 2016-02 | 2017-10 | 2.0 |
| Anopheles arabiensis | 10.2 | 0.98 | 2014-10 | 2017-10 | 10.6 |
| Anopheles culicifacies | 9.15 | 0.88 | 2014-10 | 2017-10 | 9.3 |
| Anopheles epiroticus | 3.28 | 0.25 | 2014-10 | 2017-10 | 3.6 |
| Anopheles farauti | 6.5 | 0.75 | 2015-06 | 2017-10 | 8.4 |
| Anopheles funestus | 12.9 | 0.47 | 2014-10 | 2017-10 | 15.2 |
| Anopheles gambiae | 7.3 | 1.3 | 2016-02 | 2017-10 | 6.8 |
| Anopheles melas | 3.7 | 0.41 | 2015-06 | 2017-10 | 3.3 |
| Anopheles merus | 6.1 | 0.53 | 2015-06 | 2017-10 | 5.4 |
| Anopheles minimus | 4.21 | 0.22 | 2014-10 | 2017-10 | 4.2 |
| Anopheles quadriannulatus | 10.1 | 0.89 | 2014-10 | 2017-10 | 9.9 |
| Anopheles sinensis | 5.84 | 0.41 | 2015-06 | 2017-10 | 4.5 |
| Anopheles stephensi SDA-500 | 5.8 | 0.57 | 2014-10 | 2017-10 | 0.4 |
| Anopheles stephensi Indian | 0.37 | 2014-10 | 2017-10 | 5.0 | |
| Ixodes scapularis | 1.78 | 2015-02 | 2017-10 | 0.8 |
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. The video slides (including demo outlines), are in our regular tutorial pages.
Future releases
The next VectorBase release (VB-2017-12) is scheduled for middle December.
Other known issues
- DONE:
The gene expression BioMart database will be updated a few days after the release date. Apologies for any inconvenience. - The activation of variation tracks in the genome browser from PopBio application links do not currently work, but manual configuration of variation tracks from the within the genome browser still work as normal.
Please report any problems to the helpdesk.
Release date:
Wednesday, October 25, 2017
