Release VB-2015-02

We are pleased to announce the February release of VectorBase (VB-2015-02):

  • Gene set updates have been produced for four Glossina species. Low quality gene models that lack support have been demoted for Glossina austeni (3051 genes), G. brevipalpis (4894 genes), G. fuscipes (3123 genes) and G. pallidipes (2653 genes).
  • New variation datasets for Ixodes scapularis.
  • The latest Drosophila assembly and gene set (FlyBase 6.02) have been used to construct updates to the proten coding gene trees, and new genome pairwise alignments between D. melanogaster, Anopheles gambiae, and Aedes aegypti.
  • Whole genome pairwise alignments have been constructed between all Anophelines in the An. gambiae complex (An. arabiensis, An. coluzzii, An. gambiae, An. melas, An. merus, An.quadriannulatus), and between the different reference strains for Anopheles sinensis and Anopheles stephensi.
  • A major new differential gene expression via RNA-seq dataset has been added to the genome browser. Gene expression levels in a number of Anopheles gambiae cell lines are now available.
  • Five new Web Apollo instances are available for access through Web Apollo.
  • New versions of VectorBase-supported ontologies added to the ontology browser and also available for download.
  • Spatial search by center geo-coordinates and radius is now available in Advanced Search for Population Biology data.
  • Two new insecticide resistance studies added for South America.
  • Please note that the VectorBase Galaxy server has been changed to an HTTPS connection. Please change your bookmarks to
  • The Galaxy server has been updated to the latest software version (January 2015 Stable Release).
  • New documentation material for gene manual annotations using Web Apollo, which includes a decision tree, a video tutorial, practice exercises (in a demo site), updated FAQs and more.
  • Check our tutorials section called "Other Bioinformatic Resources", in this release it includes resources for K-12 and undergraduates in the areas of genetics, bioinformatics, phylogenetics and genomics.


VectorBase is committed to a new release every two months with all data freely available for public use based on NIH/NIAID policy. A list of these changes and the state of current versions on this date (e.g., current gene sets) can be found on the Releases section of VectorBase.

For your species of interest, click on Organism, Strain, Assembly, or Gene set to find the Genome Browser link (which looks like this:  ).

Released genomes, with gene predictions

Organism Strain Assembly Gene set Gene Count Browser
Aedes aegypti Liverpool AaegL3 AaegL3.3 17 478
Anopheles albimanus STECLA AalbS1 AalbS1.2 12 335
Anopheles arabiensis Dongola AaraD1 AaraD1.2 13 678
Anopheles atroparvus EBRO AatrE1 AatrE1.2 14 230
Anopheles christyi ACHKN1017 AchrA1 AchrA1.2 11 156
Anopheles coluzzii Mali-NIH AcolM1 AcolM1.1 14 703
Anopheles culicifacies A A-37 AculA1 AculA1.2 14 882
Anopheles darlingi Coari AdarC3 AdarC3.2 10 948
Anopheles dirus A WRAIR2 AdirW1 AdirW1.2 13 239
Anopheles epiroticus Epiroticus2 AepiE1 AepiE1.2 12 602
Anopheles farauti FAR1 AfarF1 AfarF1.2 13 703
Anopheles funestus FUMOZ AfunF1 AfunF1.2 13 756
Anopheles gambiae PEST AgamP4 AgamP4.2 13 624
Anopheles maculatus B maculatus3 AmacM1 AmacM1.2 15 046
Anopheles melas CM1001059 AmelC1 AmelC1.2 16 666
Anopheles merus MAF AmerM1 AmerM1.2 14 415
Anopheles minimus A MINIMUS1 AminM1 AminM1.2 13 128
Anopheles quadriannulatus A SANGQUA AquaS1 AquaS1.2 13 857
Anopheles sinensis China AsinC2 AsinC2.1 19 815
Anopheles sinensis SINENSIS AsinS1 AsinS1.2 15 280
Anopheles stephensi Indian AsteI2 AsteI2.2 12 350
Anopheles stephensi SDA-500 AsteS1 AsteS1.2 13 650
Culex quinquefasciatus Johannesburg CpipJ2 CpipJ2.2 19 363
Glossina austeni TTRI GausT1 GausT1.2 20 333
Glossina brevipalpis IAEA GbreI1 GbreI1.2 15 022
Glossina fuscipes IAEA GfusI1 GfusI1.2 20 749
Glossina morsitans Yale GmorY1 GmorY1.4 12 962
Glossina pallidipes IAEA GpalI1 GpalI1.2 19 844
Ixodes scapularis Wikel IscaW1 IscaW1.4 20 771
Musca domestica Aabys MdomA1 MdomA1.1 15 803
Pediculus humanus USDA PhumU2 PhumU2.1 11 699
Rhodnius prolixus CDC RproC1 RproC1.3 17 244

Pre-released genomes, with mapped data and gene predictions

Organism Strain Assembly Gene set Gene Count Browser
Biomphalaria glabrata BB02 BglaB1 BglaB1.2 14 351
Lutzomyia longipalpis Jacobina LlonJ1 LlonJ1.1 10 429
Phlebotomus papatasi Israel PpapI1 PpapI1.1 12 678

Expression Data

RNA-seq data from the NIAID Arthropod Vector Cell line transcriptome (AVCL) consortium has been added to the Expression Browser - in addition to an experiment comparing gene expression in various cell lines from MR4, two experiments probe the responses to viral and Wolbachia infection.

Population Biology/Insecticide Resistance

Two new baseline studies on Anopheles nuneztovari and Anopheles darlingi insecticide resistance have been added. More recent data from these researchers will be added at a later date.

Metadata for samples in the genome browser with variation data has been added to PopBio for a subset of the 16 recently sequenced Anopheles species, Ixodes scapularis and Aedes aegypti. See projects VBP0000119, VBP0000120 and VBP0000121.

Variation Data

New data

New variation data sets are available for Ixodes scapularis Florida and Virginia populations.


Summary of available variation data by organism

    Reference species SNP calls (million) Indel calls (million) Last updated
    Aedes aegypti 0.28 0.004 2014-10
    Anopheles arabiensis 10.2 0.98 2014-10
    Anopheles culicifacies 9.15 0.88 2014-10
    Anopheles epiroticus 3.28 0.25 2014-10
    Anopheles funestus 12.9 0.47 2014-10
    Anopheles gambiae 7.3 1.3 2014-10
    Anopheles minimus 4.21 0.22 2014-10
    Anopheles quadriannulatus 10.1 0.89 2014-10
    Anopheles stephensi SDA-500 5.8 0.57 2014-10
    Anopheles stephensi Indian 0.37 2014-10
    Ixodes scapularis 1.78 2015-02

    Mitochondrial gene summaries for VectorBase genera

    Links to Mitochondrial data for the 4 main genera are presented below for convenience.

    Genus/genera Reference species Mitochondrial gene resource Last updated
    Aedes Aedes aegypti Aedine mitochondrial genes 2014-08
    Anopheles Anopheles gambiae Anopheline mitochondrial genes 2014-08
    Culex Culex quinquefasciatus Culicine mitochondrial genes 2014-08
    Ixodidae and Argasidae Ixodes scapularis Ixodida mitochondrial genes 2014-08


    Follow this link for the tutorials page, which also includes videos, practice exercises, and sample files.

    Known issues

    • The Anopheles quadriannulatus reference strain has been updated in this release from SANGWE to SANGQUA (the SANGWE strain is a synonym for SANGQUA).
    • Some issues are being resolved with the Anopheles gambiae "median shifted mean" expression data and expression map.
      Download files fixed.
      Three expression maps are now available for Anopheles gambiae:
      • The default map has the same experimental data as last release - the new cell-line data is excluded.
      • This map has the same data as above PLUS the RNA-Seq cell-line data - note that 800+ genes with "mostly zero" expression are heavily affecting the clustering.
      • Finally, there's a map made with just the cell-line data. Again the clustering is influenced by the 800+ genes apparently not expressed in the cell lines.
    • Some link-outs from the Expression BioMart results are currently misconfigured and are not working correctly. Fixed 2015-02-20.

    Please report any problems to the helpdesk.

    Release date: 
    Thursday, February 19, 2015