Release VB-2016-02

We are pleased to announce the February 2016 release of VectorBase (VB-2016-02):

  • Genome and gene set for Aedes albopictus (Foshan strain).
  • New variation data (copy number variants and SNPs) linked to deltamethrin resistance in Aedes aegypti.
  • New variation data for Anopheles gambiae populations from Burkina Faso.
  • New alignments of Rfam covariance models for structural RNA elements, in all species.
  • Upgrade to WebApollo software v2.0.1
  • New Anopheles gambiae mass spectrometry data set added.
  • Better integration of assembled transcriptomes and mass spec. proteome data with keyword search and BLAST.
  • New WebApollo gene annotation track in genome browsers to allow public display of ongoing WebApollo edits.

    N.B. WebApollo identifiers shown on the track are not stable identifiers and must not be used in publications referencing data as they may be deprecated without warning. If you require stable annotation IDs for WebApollo gene model edits, please contact VectorBase directly.

  • New download files for all types of comparative data.
  • Updated versions for the following tutorials: Submit, Tour and, Search.
  • Updated population biology start page

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 AcolM1.2 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 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 BglaB1.3 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 the Foshan strain of the Aedes albopictus genome is fully released, including a whole genome alignment with Aedes aegypti. Covariance models from Rfam (release 12.0) have been aligned against all species and made available as a track in the genome browser. Gene descriptions were propagated from well-annotated species to closely related species. In cases where miRNA genes overlap on opposite strands, the gene description now includes an explanatory note. Data can be accessed either via the genome browser for each species, or via BioMart.

All of the comparative data in VectorBase (gene trees, homologs, and pairwise whole genome alignments) are now available for download as Newick, PhyloXML, OrthoXML, and MAF format files.

Whole genome alignments between Drosophila melanogaster and three species (Aedes aegypti, Anopheles gambiae, Culex quinquefasciatus) have been removed due to technical problems with their presentation, and will not be supported in the future. All of these alignments are instead available in Ensembl Metazoa.

Expression Data

A new An. gambiae mass spectrometry dataset has been added from the publication Champion M.M., Sheppard A.D., Rund S.S.C., Freed S.A., O’Tousa J.E. and Duffield G.E. (2015) Qualitative and quantitative proteomics methods for the analysis of the Anopheles gambiae mosquito proteome.

Population Biology/Insecticide Resistance

  • PopBio start page updated to provide better visibility of key tools.
  • PopBio Map:
    • Legend entries (click the [i] bottom right) are now sorted by color for easier identification.
    • Various bug fixes and optimizations.

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

    In this release we have added new variation data for Aedes aegypti and Anopheles gambiae. Data on SNP and Copy Number Variation variants linked to deltamethrin resistance in Aedes aegypti have been added from the recent paper "Identifying genomic changes associated with insecticide resistance in the dengue mosquito Aedes aegypti by deep targeted sequencing." by Faucon et al. We have also added population variation data for Anopheles gambiae in Burkina Faso as described in the paper "Genetic Structure of a Local Population of the Anopheles gambiae Complex in Burkina Faso." by Markianos et al.

    Tutorials

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


    Future releases

    The next VectorBase release (VB-2016-04) is scheduled for late April.

    In the April release of VectorBase (VB-2016-04) we intend to:

    • Better integrate transcriptome and other non-genome linked data through search,
    • Retire mass spectrometry tracks showing alignments directly to the genome, in favor of alignments to the proteome to minimize the number of low quality mappings. The following DNA alignment tracks will be retired:
    • Retire remaining DAS annotation sources
    • Distributed Annotation Server (DAS) tracks will no longer be supported as of the April release. The following tracks will therefore be retired


    Known issues

    Retirement of DAS annotation sources

    Distributed Annotation Server (DAS) track support is in the process of being phased out, and will no longer be supported as of the April release. The following tracks have removed in this release as they are either no longer active, or the data has been duplicated in existing browser tracks.

    Other known issues

    • Newly added genomic variation data is not yet linked with the sample metadata in the population biology browser. This will be available in the next release.
    • The species identification protocols and metadata for population biology project VBP0000124 (Markianos et al) are not entirely accurate and will be updated for the next release.

    Please report any problems to the helpdesk.

    Release date: 
    Wednesday, February 24, 2016