Release VB-2015-06

Submitted by creinkin on Fri, 2015-05-15 10:27

We are pleased to announce the June release of VectorBase (VB-2015-06):

  • New genome assemblies, variation databases and gene patch builds for Anopheles farauti, Anopheles melas, Anopheles merus and Anopheles sinensis
  • New gene patch builds for Phlebotamus papatasi, Lutzomyia longipalpis and Anopheles funestus
  • New organism added - Glossina palpalis
  • New or updated whole genome alignments have been added for 30 organism pairs in this release
  • New host-choice expression data for Aedes aegypti
  • Login Authentication has been updated. If you experience any issues, try to reset your password first. If still unsuccessful please email info@vectorbase.org
  • New documentation for the BioMart tutorial including new slides and practice exercises for the gene database with its corresponding answer key.

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:  ).

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 AalbS1.2 12 335
Anopheles arabiensis Dongola AaraD1 AaraD1.2 13 678
Anopheles atroparvus EBRO AatrE1 AatrE1.2 14 230
Anopheles christyi ACHKN1017 AchrA1 AchrA1.2 11 156
Anopheles coluzzii Mali-NIH AcolM1 AcolM1.1 14 703
Anopheles culicifacies A A-37 AculA1 AculA1.2 14 882
Anopheles darlingi Coari AdarC3 AdarC3.2 10 948
Anopheles dirus A WRAIR2 AdirW1 AdirW1.2 13 239
Anopheles epiroticus Epiroticus2 AepiE1 AepiE1.2 12 602
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 AminM1.2 13 128
Anopheles quadriannulatus A SANGQUA AquaS1 AquaS1.2 13 857
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 AsteS1.2 13 650
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 RproC1 RproC1.3 17 244

In this release the genome assemblies for Anopheles farauti, Anopheles melas, Anopheles merus and Anopheles sinensis were updated to the latest versions, and the gene sets for sandflies Phlebotamus papatasi, and Lutzomyia longipalpis have moved from pre-release to full release status. Community supplied gene annotations were also updated for the anophelines Anopheles farauti, Anopheles funestus, Anopheles melas, Anopheles merus and Anopheles sinensis, and the for the sandflies Phlebotamus papatasi, Lutzomyia longipalpis. A new organism Glossina palpalis has also been added in this release.

For the four Anopheline species with new assemblies, genes were projected from the old assemblies via an assembly alignment with ATAC. For Anopheles farauti, 13,469 (98.2%) transcripts were projected; for Anopheles melas, 15,851 (95.1%); for Anopheles merus, 13,806 (95.7%); and for Anopheles sinensis 13,331 (87.3%). For each species a set of files is available which contains full details of the transcripts that did/didn't get projected (and why). The README files (e.g. for An. farauti) describe the projection methodology and outline the resources available for reinstating genes that were unable to be projected automatically. A track has been added to the WebApollo instances for these species showing unprojected transcripts that partially map to the new assembly.

Thirty whole genome alignments were generated for this release. Six of these alignments are between the new species Glossina palpalis and the other Glossinidae + Musca domestica. Nine realignments were necessary within the gambiae complex, due to the new assemblies for Anopheles melas and Anopheles merus. Finally, 15 tBLAT alignments were replaced by LASTZ alignments. LASTZ typically gives about twice the coverage for non-coding regions, and increases coverage in coding regions by a lesser, but still significant amount (up to about 10%). Statistics on coverage for each pairwise alignment are available via the complete list of alignments.

Expression Data

The Aedes aegypti RNA-seq expression data from the publication Evolution of mosquito preference for humans linked to an odorant receptor by McBride and coauthors is now available in the Expression Browser. The data is represented in VectorBase as two "experiments":

Population Biology/Insecticide Resistance

Several large datasets have been overhauled to improve the storage and representation of species and inversion genotype data. More specifically projects VBP0000003, VBP0000005, VBP0000006 and VBP0000008 have had their inversion genotype representation improved so that the inverted allele counts are now available for all genotyped samples. An issue with our species taxonomy has been corrected, such that samples from these projects are now correctly assigned to species based on their Scott and Favia/Fanello PCR tests. Several minor curation issues were fixed in other projects.

Variation Data

New data

New variation data added for Anopheles farauti, Anopheles melas, Anopheles merus and Anopheles sinensis from the paper "Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes."

Updates

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 2015-06
    Anopheles culicifacies 9.15 0.88 2014-10 2015-06
    Anopheles epiroticus 3.28 0.25 2014-10 2015-06
    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 2015-06
    Anopheles quadriannulatus 10.1 0.89 2014-10 2015-06
    Anopheles sinensis 5.84 0.41 2015-06 2015-06
    Anopheles stephensi SDA-500 5.8 0.57 2014-10 2015-06
    Anopheles stephensi Indian 0.37 2014-10 2015-06
    Ixodes scapularis 1.78 2015-02 2015-06


    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

    Tutorials

    Follow this link for the tutorials page, which also includes videos, practice exercises, and sample files. In this release there is only one update to an existing tutorial (BioMart) due to the maternity leave of our outreach coordinator


    Known issues

    Please report any problems to the helpdesk.

    Release date: 
    Wednesday, June 24, 2015