Release VB-2016-08

We are pleased to announce the August 2016 release of VectorBase (VB-2016-08):

  • Four RNA-seq differential expression experiments have been added for Aedes albopictus, Ae. aegypti, Anopheles gambiae and Musca domestica.
  • Five new insecticide resistance datasets added to the Population Biology resource.
  • PopBio map: new custom data download facility and improved insecticide resistance coloring
  • New gene model updates from the community for An. coluzzii and B. glabrata.
  • New gene set update for M. domestica from the NCBI Annotation Release 101.
  • New RNAseq functionality with improved search, alignments, track hubs and a tutorial. Please also see the future releases section at the end of these release notes for details of the retirement of old RNAseq search and display functions.
  • The strain name for the files in the download section for An. quadriannulatus have been updated to SANGQUA from SANGWE. This brings the nomenclature used on the site into line with the most recent scientific literature.
  • STRING (PMID:25352553) protein-protein interaction database cross references have been added for Ae. aegypti (9333), An. darlingi (4555), An. gambiae (7872), Cx. quinquefasciatus (11109) and Ixodes scapularis (9349). STRING records can be viewed either via the transcript records for each gene in the genome browser (e.g. AGAP004707-RA), or retrieved in bulk via BioMart.
  • Integrated mass spec data now directly accessible from the Proteome resource
  • New Zika Organism Resource page provides background information about the Zika virus, some recent news/social media about the virus, and links to helpful resources and publications hosted on VectorBase and/or other websites.
  • Some changes were made to the scheduling back-end of BLAST queries to increase efficiency. In general, VectorBase users should observe a considerable improvement in the response time.
  • A new Comparative Genomics video tutorial has been created

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 AalbS1 AalbS1.3 12 509
Anopheles arabiensis Dongola AaraD1 AaraD1.3 13 849
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 AfunF1.3 13 884
Anopheles gambiae PEST AgamP4 AgamP4.3 13 793
Anopheles maculatus B maculatus3 AmacM1 AmacM1.3 15 050
Anopheles melas CM1001059 AmelC2 AmelC2.1 15 850
Anopheles merus MAF AmerM2 AmerM2.1 13 798
Anopheles minimus MINIMUS1 AminM1 AminM1.3 13 231
Anopheles quadriannulatus A SANGWE AquaS1 AquaS1.3 13 992
Anopheles sinensis China AsinC2 AsinC2.1 19 815
Anopheles sinensis SINENSIS AsinS2 AsinS2.1 13 331
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

The four new RNA-seq differential expression experiments are:

Population Biology/Insecticide Resistance

Five insecticide resistance papers have been added:

  • Insecticide resistance status in Culex quinquefasciatus in Benin
    VBP0000133
  • Knockdown resistance of Anopheles sinensis in Henan province, China
    VBP0000134
  • Contrasting patterns of insecticide resistance and knockdown resistance (kdr) in the dengue vectors Aedes aegypti and Aedes albopictus from Malaysia
    VBP0000135
  • Multi-country Survey Revealed Prevalent and Novel F1534S Mutation in Voltage-Gated Sodium Channel (VGSC) Gene in Aedes albopictus
    VBP0000136
  • Nationwide assessment of insecticide susceptibility in Anopheles gambiae populations from Zimbabwe
    VBP0000137

These are all available in the PopBio map which now has a newly added data download facility.


The coloring of insecticide resistance has been improved. Measures of lethal time and concentration have been log-transformed to make better use of the color scale. Percent mortality data also now uses a nonlinear color scale mapping. Please see the online help text in the legend (bottom right [i] icon) for more details.

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 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 tutorials for this release are:


    Future releases

    The next VectorBase release (VB-2016-10) is scheduled for late October.

    The old and new RNAseq display and discovery systems will run alongside each other until the December 2016 release, after which the old RNAseq tracks and display options will be retired on the site. This means that the following page will be removed as it’s functionality will have been replaced by the RNAseq site search

     https://www.vectorbase.org/rna-seq-data-sets

    The existing RNAseq tracks in the genome browser will also be removed in favour of the tracks generated by the HISAT pipeline. If you believe this will be a problem for your work please contact us and we will ensure that the old alignments continue to be made available after the December 2016 release.

    Other known issues

    • WebApollo will be updated independent of this release. Please ask if you have questions with this plan.

    Please report any problems to the helpdesk.

    Release date: 
    Thursday, August 25, 2016