Release VB-2015-10

Submitted by creinkin on Wed, 2015-10-14 12:45

We are pleased to announce the October release of VectorBase (VB-2015-10):

  • Genome and gene set for Stomoxys calcitrans.
  • Updated gene sets for Anopheles gambiae, Anopheles christyi, Anopheles culicifacies, Anopheles darlingi and Anopheles maculatus.
  • Recalculated variation effects to reflect gene model changes for Anopheles species.
  • Remapped funcgen probes to reflect gene model changes for Anopheles gambiae.
  • President's Malaria Initiative insecticide data: full release
  • New expression data for Anopoheles funestus
  • AGP files available for download have been regenerated, according to version 2.0 of the AGP specification
  • GTF files for all species with annotated genes have been regenerated, according to version 2.2 of the GTF specification
  • The Ontology for Vector Surveillance and Management (VSMO) added to our Ontolgy browser to support emerging projects
  • Finally, out-dated protein alignments were removed from the genome broswer for Aedes aegypti, Anopheles coluzzii, Anopheles gambiae, Culex quinquefasciatus, and Ixodes scapularis.
  • Updated the PopBio Advanced Search structure with hopes of making it easier to find anything PopBio related

Genomes

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 AalbS1.3 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 SDA-500 AsteS1 AsteS1.3 13 764
Anopheles stephensi Indian AsteI2 AsteI2.2 12 350
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
Glossina palpalis IAEA GpapI1 GpapI1.0 20 725
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
Stomoxys calcitrans USDA ScalU1 ScalU1.1 16 636

In this release a new database has been created for Stomoxys calcitrans (a comparator species for Tsetse fly), and there have been updates to genes sets for multiple Anopheles species. The latest gene set updates have been derived from community supplied gene annotations for Anopheles gambiae, Anopheles christyi, Anopheles culicifacies, Anopheles darlingi and Anopheles maculatus. Data can be accessed either via the genome browser for each species, or via BioMart.

Expression Data

Two new experiments have been added, one microarray experiment looking at gene expression differences between permethrin resistant Anopheles funestus mosquitoes from Mozambique and Malawi and an RNA-seq experiment investigating the gene expression response in Anopheles gambiae to blood meals containing ivermectin.

Population Biology/Insecticide Resistance

The President's Malaria Initiative insecticide resistance dataset has been updated to fix a few curation errors. The new PopBio map now contains help text and other small fixes and improvements.


Meta-projects have been removed from the database/website. These were a little-used feature and the new map is a much more powerful tool to explore data from multiple projects at once.

Variation Data

New data.

No new data has been added this release.

Updates.

Variation consequences have been updated for Anopheles gambiae and Anopheles culicifacies based on the gene model updates for these species.

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 the Downloads section, AGP files for all species with assembled genomes have been regenerated, according to version 2.0 of the AGP specification; and GTF files for all species with genes have been regenerated, according to version 2.2 of the GTF specification.

    Out-dated protein alignments (mostly taxonomically-stratified sections of the UniProt database that were several years old) were removed from the genome broswer for Aedes aegypti, Anopheles coluzzii, Anopheles gambiae, Culex quinquefasciatus, and Ixodes scapularis.

    Tutorials

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


    Future releases

    The next VectorBase release (VB-2015-12) is scheduled for late December.

    In the December release of VectorBase (VB-2015-12) we intend to at least:

  • update gene models for the Glossina species based on the annotation workshop held in Kenya earlier this year
  • begin to upgrade our Web Apollo instances to version 2.0 of this software
  • better integrate RNAseq data and documentation in the VectorBase resource
  • continue to make improvements to the search and Population Biology interfaces


    • Known issues

    • The Expression Maps have been delivered a few days late this release. Sorry for any inconvenience caused.

    Please report any problems to the helpdesk.

    Release date: 
    Wednesday, October 21, 2015