Release VB-2015-12

We are pleased to announce the December release of VectorBase (VB-2015-12):

  • Genome and gene set for Sarcoptes scabiei var canis
  • Updated gene sets for Glossina austeni, Glossina brevipalpis, Glossina fuscipes, Glossina morsitans, Glossina pallidipes and Glossina palpalis
  • Migration of community annotation projects to the latest Web Apollo v2 release. A short new tutorial describes the key differences between the two versions.
  • Data-only release of Aedes albopictus (Foshan strain): the genome sequence and gene set are available for download.
  • Variation data links added to the Ag1000G Anopheles gambiae 1000 genomes project
  • GFF3 geneset files have been regenerated, according to the Sequence Ontology specifications.
  • Repeat features are now available for download, in GFF3 format.
  • Updated versions for the following tutorials: Available data types, BioMart, Genome Browser, HMMER and Search.

Genomes

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 AalbS1.3 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 AcolM1.2 14 711
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 SANGQUA AquaS1 AquaS1.3 13 992
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 BglaB1.3 14 423
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 MdomA1.1 15 803
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

In this release a new database has been created for Sarcoptes scabiei, and there have been updates to genes sets for multiple Glossia species. The latest gene set updates have been derived from community supplied gene annotations for Glossina austeni, Glossina brevipalpis, Glossina fuscipes, Glossina morsitans,Glossina pallidipes and Glossina palpalis. Data can be accessed either via the genome browser for each species, or via BioMart.

EST and RNA-seq data have been aligned against the Stomoxys calcitrans genome, and the alignments are available as tracks in the genome browser.

The Aedes albopictus genome and gene set are available in the Downloads section, which also includes updated GFF3 files for all species with gene sets.

For comparative analyses, species are now stratified in a more fine-grained manner, into the following groups: Anophelinae, Culicinae, Phlebotominae, Brachycera, Hemiptera, Phthiraptera, Chelicerata, Gastropoda. This enables orthologs to be filtered at each of these taxonomic levels, and gene trees are now colored according to these groups (further details).

Expression Data

No new data has been added but an issue with Advanced Search of expression data has now been fixed. It is now possible to search/filter with high level taxonomic terms (such as "genus Culex") in the species field. Download files and resources marked "VB-2015-10" are still current and are consistent with rest of VectorBase.

Population Biology/Insecticide Resistance

The President's Malaria Initiative insecticide resistance dataset has been re-imported one more time to fix some small issues and also to include a small number of assays that determined mutant kdr gene frequencies.

Variation Data

No new data has been added this release.

Summary of available variation data by organism

    Reference species SNP calls (million) Indel calls (million) Last dataset update Last variation effect update
    Aedes aegypti 0.31 0.004 2015-04 2015-06
    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 2014-10 2015-10
    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

    In this release we have added links from variation data for Anopheles gambiae to the Ag1000G Anopheles 1000 Genomes project. Ag1000G is a global collaboration using whole genome deep sequencing to provide a high-resolution view of genetic variation in natural populations of Anopheles gambiae, the principal vector of Plasmodium falciparum malaria in Africa. For a more information about the Anopheles 1000 Genomes project please see the main Ag1000G website.

    To access this data follow the "View variant in Ag1000G browser" link on any variant summary page (see example). Please note that some variants in the VectorBase variation database may not link to a corresponding entry in the Ag1000G project as the VectorBase and Ag1000G resources are distinct, but complementary.

    Tutorials

    We have added one new tutorial for this release:

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


    Future releases

    The next VectorBase release (VB-2016-02) is scheduled for late February.

    In the February release of VectorBase (VB-2016-02) we intend to include:

    • Full release of Aedes albopictus (Foshan strain)
    • Further improvement of WebApollo2 resource
    • New CNV data related to insecticide resistance in Aedes aegypti
    • Improved integration of annotated transcriptome and MS peptide datasets (retiring the GDAV system)


    Known issues

      Please report any problems to the helpdesk.

      Release date: 
      Tuesday, December 15, 2015