Release VB-2015-08

We dedicate this release of VectorBase to founding member Bill Gelbart - a professor, advisor, leader in genetics research, and an active member of the Genetics Society of America. Bill also served in various roles for such projects as FlyBase, WormBase, as well as being on the National Advisory Council for the National Human Genome Research Institute.

See the full memoriam article here.

For this August release of VectorBase (VB-2015-08), we have:

  • Updated Rhodnius prolixus assembly and gene set now available (see the Genomes section of these release notes for full details)
  • Updated gene sets for Anopheles albimanus, Anopheles arabiensis, Anopheles atroparvus, Anopheles coluzzii, Anopheles dirus, Anopheles epiroticus, Anopheles minimus, Anopheles quadriannulatus and Anopheles stephensi.
  • Variation effects recalculated to reflect gene model changes for Anopheles species
  • A new video tutorial (10 min) titled "Genetic Variation data" is available.
  • New preview/prototype population biology/insecticide resistance map search tool available for testing.
  • Data from the President's Malaria Initiative (PMI), has been loaded as preliminary (see Population Biology section of these release notes for full details)
  • There is a video tutorial (16 min) and practice exercises with their answer keys for PopBio new map and the tool in general.

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 AchrA1.2 11 156
Anopheles coluzzii Mali-NIH AcolM1 AcolM1.2 14 711
Anopheles culicifacies A A-37 AculA1 AculA1.2 14 882
Anopheles darlingi Coari AdarC3 AdarC3.2 10 948
Anopheles dirus A 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 AgamP4.2 13 624
Anopheles maculatus B maculatus3 AmacM1 AmacM1.2 15 046
Anopheles melas CM1001059 AmelC2 AmelC2.1 15 850
Anopheles merus MAF AmerM2 AmerM2.1 13 798
Anopheles minimus A 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

The Rhodnius prolixus assembly has been updated from version RproC1 to RproC3. RproC1 was in fact version 2 of the assembly according to INSDC (version 1 was a contig only assembly that was never hosted by VectorBase), so we have taken this opportunity to align our versioning with INSDC. The RproC1 gene set has been projected onto the new assembly; 98% of the transcripts were projected, full statistics are available in the Downloads section. In previous VectorBase releases, preliminary RNA-seq datasets had been aligned against RproC1, for display as tracks in the genome browser; the full set of RNA-seq experiments and a transcriptome have now been submitted to the sequence archives, and these were aligned against the new assembly.

In this release 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 albimanus, Anopheles arabiensis, Anopheles atroparvus, Anopheles coluzzii, Anopheles dirus, Anopheles epiroticus, Anopheles minimus, Anopheles quadriannulatus, and Anopheles stephensi. Data can be accessed either via the genome browser for each species, or via BioMart.

Chromosome, scaffold and contig Fasta files for all species with assembled genomes have been regenerated, to ensure that softmasking reflects the current repeat annotation, and to ensure consistency in the formatting of headers. For reference, these Fasta files have the header structure:

>[identifier] [data_type]:[sequence_type] [sequence_type]:[assembly]:[sequence_id]:[start]:[end]:[strand]

For example:

>AAGE02013910.1 dna:contig contig:AaegL3:AAGE02013910.1:1:685587:1

Expression Data

Unusually, and for operational reasons, no updates at all have been made this release. Please continue to use the expression resources labeled VB-2015-06, which are still current and correct.

Population Biology/Insecticide Resistance

An early preview version of the new PopBio/IR map interface is now available. In addition, new insecticide resistance data from the President's Malaria Initiative has been loaded in preliminary curation status. Some details still need to be fixed before we make a more formal announcement of this at the October release.

Variation Data

New data

No new data has been added this release.

Updates

Variation consequences have been updated for Anopheles arabiensis, Anopheles epiroticus, Anopheles minimus, Anopheles quadriannulatus and Anopheles stephensi 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 2015-06
    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 2015-06
    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

    Tutorials

    Follow this link for the latest tutorials, which also includes videos, practice exercises, and sample files. Our outreach coordinatorIn is back from her maternity leave.


    Future releases

    The next VectorBase release (VB-2015-10) is scheduled for late October.

    In the October release of VectorBase (VB-2015-10) we intend to remove tracks from the genome browser that display out-dated protein alignments. These are mostly taxonomically-stratified sections of the UniProt database that haven't been updated in several years, and these protein sets are sufficiently out-of-date that the tracks are no longer useful. The affected species are: Aedes aegypti, Anopheles coluzzii, Anopheles gambiae, Culex quinquefasciatus, and Ixodes scapularis. If you have any questions or concerns about this change, please contact us.


    Known issues

    Please report any problems to the helpdesk.

    Release date: 
    Wednesday, August 26, 2015