Release VB-2015-04

We are pleased to announce the April release of VectorBase (VB-2015-04):

  • Several new changes and updates have been incorporated and can be visualized using the Genome Browser including:
    • New variation datasets for Aedes aegypti
    • Pairwise alignments for all Glossina species and Musca domestica created, viewable through the 'Comparative Genomics' section in the Genome Browser, and summarized at As shown in the following two links/examples, to check the updates in your gene of interest go to the gene page, and in the gene or location tabs click on "Comparative Genomics" under the left hand side menu
    • Community gene model updates added for Biomphalaria glabrata
    • Projected gene descriptions added for Anopheles and Glossina species
    • Protein features reannotated in all species. To check the updates in your gene of interest go to the gene page, click on the transcript tab and under the left hand side menu go to "Protein Information/Domanis & Features", as shown in this example
    • Improved Trinity RNASeq alignments added for Glossina brevipalpis, G. fuscipes and G. palidipes in the "Trinity-assembled transcripts" track in the "RNAseq alignments" category of the Genome Browser
    • Community annotation cross references updateds for all species. To check the updates in your gene of interest go to the gene page and under the left hand side menu click on "External References", as shown in this example
  • Three microarray experiments relating to the reproductive tract of Anopheles gambiae mosquitoes have been added to the Expression Browser
  • Beta release of new search facility for scaffold or supercontig identifiers. Give it a try using the Search box and the identifier supercont1.190 - Feedback welcome
  • Made minor updates to the VectorBase content management system, search system and tools
  • New documentation for both the Web Apollo and the Expression (microarray and RNAseq) tutorials


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
Biomphalaria glabrata BB02 BglaB1 BglaB1.3 14 423
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
Lutzomyia longipalpis Jacobina LlonJ1 LlonJ1.1 10 429
Phlebotomus papatasi Israel PpapI1 PpapI1.1 12 678

In this release gene descriptions were projected from well-annotated species to other (reasonably closely-related) species, based on orthologies derived from VectorBase gene trees. For a description to be projected, a pair of orthologs must have >30% amino acid sequence identity and >66% sequence coverage. The species and gene ID from which a description is projected is included in the text of the new description. Descriptions were projected from 1) Anopheles gambiae to the other Anophelines; 2) Glossina morsitans to the other Glossinidae + Musca domestica; 3) Drosophila melanogaster to the Glossinidae + M. domestica.

Expression Data

The three new experiments are

We have not regenerated the Anopheles gambiae cell-line only expression map for this release, but will do so in future release as required.

Population Biology/Insecticide Resistance

The population browser now contains metadata for 160 Aedes aegypti mosquitoes whose SNP chip-derived genotypes are available in the genome browser.

Variation Data

New data

New variation data added for Aedes aegypti form the paper "A multipurpose high throughput SNP chip for the dengue and yellow fever mosquito, Aedes aegypti"


Summary of available variation data by organism

    Reference species SNP calls (million) Indel calls (million) Last updated
    Aedes aegypti 0.31 0.004 2015-04
    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. In this release these are the updates:

    • Web Apollo: New features include a list of access points of interest for the ~50 min general video overview and a new video clip (of ~ 2:45 min) titled "Merging models and setting intron/exon boundaries".
    • Expression (microarray and RNAseq): The tutorial slides have been updated to reflect the incorporation of RNAseq data and new display features.

    Known issues

    Please report any problems to the helpdesk.

    Release date: 
    Wednesday, April 22, 2015