Release VB-2016-12

We are pleased to announce the December 2016 release of VectorBase (VB-2016-12):

Genomes

Released genomes, with gene predictions

Organism Strain Assembly Gene set Gene Count Browser
Aedes aegypti Liverpool AaegL3 AaegL3.3 17 478
Aedes albopictus Foshan AaloF1 AaloF1.1 17 592
Anopheles albimanus STECLA AalbS2 AalbS2.1 12 521
Anopheles arabiensis Dongola AaraD1 AaraD1.4 13 908
Anopheles atroparvus EBRO AatrE1 AatrE1.3 14 244
Anopheles christyi ACHKN1017 AchrA1 AchrA1.3 11 162
Anopheles coluzzii Mali-NIH AcolM1 AcolM1.3 14 560
Anopheles culicifacies A A-37 AculA1 AculA1.3 14 889
Anopheles darlingi Coari AdarC3 AdarC3.3 10 961
Anopheles dirus WRAIR2 AdirW1 AdirW1.3 13 299
Anopheles epiroticus Epiroticus2 AepiE1 AepiE1.3 12 705
Anopheles farauti FAR1 AfarF2 AfarF2.1 13 462
Anopheles funestus FUMOZ AfunF1 AfunF1.4 13 919
Anopheles gambiae PEST AgamP4 AgamP4.4 13 807
Anopheles maculatus B maculatus3 AmacM1 AmacM1.3 15 050
Anopheles melas CM1001059_A AmelC2 AmelC2.2 15 813
Anopheles merus MAF AmerM2 AmerM2.2 13 718
Anopheles minimus MINIMUS1 AminM1 AminM1.3 13 231
Anopheles quadriannulatus A SANGWE AquaS1 AquaS1.4 14 011
Anopheles sinensis SINENSIS AsinS2 AsinS2.1 13 331
Anopheles sinensis China AsinC2 AsinC2.1 19 815
Anopheles stephensi Indian AsteI2 AsteI2.2 12 350
Anopheles stephensi SDA-500 AsteS1 AsteS1.3 13 764
Biomphalaria glabrata BB02 BglaB1 BglaB1.4 14 420
Cimex lectularius Harlan ClecH1 ClecH1.2 14 085
Culex quinquefasciatus Johannesburg CpipJ2 CpipJ2.2 19 363
Glossina austeni TTRI GausT1 GausT1.3 20 309
Glossina brevipalpis IAEA GbreI1 GbreI1.3 15 032
Glossina fuscipes IAEA GfusI1 GfusI1.3 20 737
Glossina morsitans Yale GmorY1 GmorY1.5 13 034
Glossina pallidipes IAEA GpalI1 GpalI1.3 19 852
Glossina palpalis IAEA GpapI1 GpapI1.1 20 726
Ixodes scapularis Wikel IscaW1 IscaW1.4 20 771
Lutzomyia longipalpis Jacobina LlonJ1 LlonJ1.2 10 494
Musca domestica Aabys MdomA1 MdomA1.2 16 087
Pediculus humanus USDA PhumU2 PhumU2.1 11 699
Phlebotomus papatasi Israel PpapI1 PpapI1.2 12 685
Rhodnius prolixus CDC RproC3 RproC3.1 16 843
Sarcoptes scabiei var. canis Arlian SscaA1 SscaA1.1 10 679
Stomoxys calcitrans USDA ScalU1 ScalU1.1 16 636

Expression data

A new dataset has been added for Aedes aegypti: Mosquito-microsporidia interactions (Desjardins et al., 2014).

An existing dataset has been updated to reflected the new gene set for the house fly. Explore the expression data here via site search.

Population Biology/Insecticide Resistance

We have incorporated a major new dataset from a publication by Jeff Powell's group consisting of microsatellite repeat length polymorphism data for 3,708 Aedes aegypti mosquitoes with PopBio project ID VBP0000138. In total, over 88,000 genotypes are available for download through Site Search and its Export Results feature. Logged in registered users can obtain up to 30,000 records per download. You may need to use the Advanced Search filters to restrict by Collection Site (e.g. "Africa" or a country name) or microsatellite locus using the Genotype Name field.

Collection sites can be visualised on the PopBio map by filtering for the project ID, VBP0000138. The development of new visualisation tools for genotypes and population structure is planned for 2017.

Seven insecticide resistance papers have been added:

These are all available in the PopBio map, Search and the new Sample Explorer.

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 2016-02
    Anopheles arabiensis 10.2 0.98 2014-10 2015-08
    Anopheles culicifacies 9.15 0.88 2014-10 2015-10
    Anopheles epiroticus 3.28 0.25 2014-10 2015-08
    Anopheles farauti 6.5 0.75 2015-06 2015-06
    Anopheles funestus 12.9 0.47 2014-10 2015-06
    Anopheles gambiae 7.3 1.3 2016-02 2016-02
    Anopheles melas 3.7 0.41 2015-06 2015-06
    Anopheles merus 6.1 0.53 2015-06 2015-06
    Anopheles minimus 4.21 0.22 2014-10 2015-08
    Anopheles quadriannulatus 10.1 0.89 2014-10 2015-08
    Anopheles sinensis 5.84 0.41 2015-06 2015-06
    Anopheles stephensi SDA-500 5.8 0.57 2014-10 2015-08
    Anopheles stephensi Indian 0.37 2014-10 2015-06
    Ixodes scapularis 1.78 2015-02 2015-06

    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 and youku Channels 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 tutorials for this release are:


    Future releases

    The next VectorBase release (VB-2017-02) is scheduled for late February.

    Other known issues

      Please report any problems to the helpdesk.

      Release date: 
      Wednesday, December 14, 2016