Release VB-2014-10

We are pleased to announce the October release of VectorBase (VB-2014-10):

  • New gene sets for four Glossina species (Glossina austeni, Glossina brevipalpis, Glossina fuscipes and Glossina pallidipes) and Anopheles sinensis China strain.
  • Updated gene set for Aedes aegypti (AaegL3.3)
  • The final IRBase studies have been transfered to the Population Biology database.
  • A new variation database for Anopheles stephensi Indian strain.
  • Please visit VectorBase Forum for information about how to rear sandflies. Videos and other materials have been prepared by members of Dr. Jesus G. Valenzuela lab in NIH. If you would like to ask questions to the authors of the material please Register in VectorBase website, this will give you the possibility to post questions in the forum.
  • A new "project/experiment" filter has been introduced in search. You'll see it after you "drill down" into either the expression or population biology domains in the "Filter Results" box.
  • Additional advanced search enhancements to facilitate the transition of IRBase into the VB population biology resource. We expect to update and add tutorials for this evolving functionality over the next few releases.

Genomes

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:  ).

Genome annotation

  • The first-pass MAKER-based annotation of the following Glossina species are available through the genome browser and Blast search/downloads.
    • Glossina austeni
    • Glossina brevipalpis
    • Glossina fuscipes
    • Glossina pallidipes
  • An import of the Chinese strain of Anopheles sinensis described by Zhou et el, BMC Genomics, 2014 ,18;15:42 is now available.
  • A gene set update for Aedes aegypti has been performed based on manual annotation (32 existing gene models were amended, 2 gene models split and one new gene model added)

Expression Data

No new experimental data has been added, however, a comprehensive re-annotation of all samples has been performed using ontology terms where appropriate. However, due to unforeseen circumstances, these ontology terms are not yet formally displayed or searchable. This will be rectified at the next release. Please also see the "Known issues" section at the end of this page.

The expression resource (browser, search, download files, BioMart and expression maps) has been updated with respect to the new gene sets, in particular AaegL3.3.

We have brought back a feature to expression experiment pages (example) - now you can search the data from each experiment via the link halfway down the page. Don't forget that Advanced Search now lets you find genes up or down-regulated in conditions/tissues or developmental stages of your choice.

Population Biology/Insecticide Resistance

The final studies from the legacy IRBase resource have been imported into the Population Biology (PopBio) database. In total, 97 of the original 144 IRBase studies have been imported as PopBio projects. The studies that were not imported had various annotation and meta-data issues (such as missing units, only relative numeric values) that would have degraded future search and analysis tools as the resource moves forward with new data.

In the coming months, the IRBase search interface will be retired. Please use Advanced Search to query the insecticide resistance data (select the "Population Biology" domain and "Insecticide Resistance Assays" subdomain). Please let us know how we can improve the resource, as work is planned in this area.

Additionally, a field based survey of Rhodnius prolixus and R. robustus species complex members has been added to PopBio.

Variation Data

New data

A new variation database has been added for the Anopheles stephensi Indian strain.

Updates

Variation transcript effects were re-evaluated this release for all species.

Summary of available variation data by organism

    Reference species SNP calls (million) Indel calls (million) Last updated
    Aedes aegypti 0.28 0.004 2014-10
    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 1.19 2014-10


    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

    Ontologies

    • No new ontologies as of this release. Note, however, we anticipate updating IDOMAL and MIRO for December

    Tutorials

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


    Known issues

    • The expression data is not currently searchable using ontology accessions, e.g. TGMA:0001036. A consequence of this is that the ontology browser will show zero counts for terms attached to expression data, e.g. TGMA:0001036 (ontology browser). This will be fixed in the December release.
    • Biomphalaria RNASeq tracks in the genome browser are currently unavailable - they will be restored as soon as possible.

    Please report any problems to the helpdesk.

    Release date: 
    Monday, October 20, 2014