Release VB-2018-08

Submitted by rwieck on Mon, 2018-08-13 08:53

We are pleased to announce the August 2018 release of VectorBase (VB-2018-08):

  • New PopBio Map Pathogen View - shows the results of detection assays for various parasites and viruses
  • Many vector abundance datasets added: North America, Southern Africa, South East Asia
  • Abundance view has new stacked bar chart look (comments welcome) and some bugs relating to date display in the charts have been fixed.
  • A page to display select metrics and statistics is available here.
  • A major infrastructure update was conducted this release - if you notice any abnormal behaviour please contact us with as detailed a description of the problem as possible.
  • The PhyloCSF track for Anopheles gambiae has been retired
  • Search for variation data has been added in this release, along with a new variation tutorial slides and document including sample cases with demo videos.
  • Registration is open for the 2nd webinar series of the year, with eight 1-hour sessions that started on August 1st and will finish on November 7th. Apply for a seat in our final (in-person) workshop of the year 2018, the registration has no cost to you thanks to Dr. Carl Lowenberger lab at the Simon Fraser University and VectorBase. Visit the Workshops, Meetings, and Webinars page for more information about other outreach events.

Genomes

Released genomes, with gene predictions

Organism Strain Assembly Gene set Gene Count Browser
Aedes aegypti Liverpool AGWG AaegL5 AaegL5.1 19 712
Aedes albopictus Foshan AaloF1 AaloF1.2 18 294
Anopheles albimanus STECLA AalbS2 AalbS2.5 12 511
Anopheles arabiensis Dongola AaraD1 AaraD1.8 13 840
Anopheles atroparvus EBRO AatrE3 AatrE3.1 14 078
Anopheles christyi ACHKN1017 AchrA1 AchrA1.6 11 150
Anopheles coluzzii Mali-NIH AcolM1 AcolM1.6 14 880
Anopheles culicifacies A A-37 AculA1 AculA1.5 14 714
Anopheles darlingi Coari AdarC3 AdarC3.7 10 976
Anopheles dirus WRAIR2 AdirW1 AdirW1.7 13 238
Anopheles epiroticus Epiroticus2 AepiE1 AepiE1.6 12 262
Anopheles farauti FAR1 AfarF2 AfarF2.4 13 325
Anopheles funestus FUMOZ AfunF1 AfunF1.8 13 920
Anopheles gambiae PEST AgamP4 AgamP4.9 13 814
Anopheles maculatus maculatus3 AmacM1 AmacM1.5 15 018
Anopheles melas CM1001059_A AmelC2 AmelC2.5 15 753
Anopheles merus MAF AmerM2 AmerM2.7 13 642
Anopheles merus MAF AmerM2 AmerM2.6 13 676
Anopheles minimus MINIMUS1 AminM1 AminM1.7 13 109
Anopheles minimus MINIMUS1 AminM1 AminM1.6 13 091
Anopheles quadriannulatus SANGWE AquaS1 AquaS1.8 13 945
Anopheles quadriannulatus SANGWE AquaS1 AquaS1.9 13 953
Anopheles sinensis China AsinC2 AsinC2.2 19 694
Anopheles sinensis SINENSIS AsinS2 AsinS2.4 13 181
Anopheles stephensi Indian AsteI2 AsteI2.3 12 189
Anopheles stephensi SDA-500 AsteS1 AsteS1.6 13 614
Biomphalaria glabrata BB02 BglaB1 BglaB1.6 31 985
Cimex lectularius Harlan ClecH1 ClecH1.3 15 292
Culex quinquefasciatus Johannesburg CpipJ2 CpipJ2.4 19 793
Glossina austeni TTRI GausT1 GausT1.6 20 103
Glossina brevipalpis IAEA GbreI1 GbreI1.6 14 989
Glossina fuscipes IAEA GfusI1 GfusI1.6 20 517
Glossina morsitans Yale GmorY1 GmorY1.8 12 853
Glossina morsitans Yale GmorY1 GmorY1.9 12 869
Glossina pallidipes IAEA GpalI1 GpalI1.6 19 665
Glossina palpalis IAEA GpapI1 GpapI1.3 20 540
Ixodes scapularis Wikel IscaW1 IscaW1.6 23 340
Lutzomyia longipalpis Jacobina LlonJ1 LlonJ1.4 10 650
Musca domestica Aabys MdomA1 MdomA1.3 16 135
Pediculus humanus USDA PhumU2 PhumU2.4 11 712
Phlebotomus papatasi Israel PpapI1 PpapI1.4 11 660
Rhodnius prolixus CDC RproC3 RproC3.3 15 738
Sarcoptes scabiei var. canis Arlian SscaA1 SscaA1.2 10 797
Stomoxys calcitrans USDA ScalU1 ScalU1.4 16 928

Expression data

New experiments processed and added to the expression browser:

Population Biology/Insecticide Resistance

A new pathogen view has been added to the map. This shows the results of pathogen presence/absence assays performed on vector samples.

25 projects have been added:

  • Targeted application of an organophosphate-based paint applied on windows and doors against Anopheles coluzzii resistant to pyrethroids under real life conditions in Vallée du Kou, Burkina Faso (West Africa) (VBP0000296: details, map, 1 collections, 2 samples, 4 phenotypes, 4 genotypes)
  • Discriminating lethal concentrations for pyrethroid compounds used in susceptibility monitoring of Anopheles epiroticus, a malaria vector in Thailand (VBP0000297: details, map, 1 collections, 1 samples, 5 phenotypes, 0 genotypes)
  • Mosquito community composition in South Africa and some neighboring countries (VBP0000298: details, map, 11 collections, 1480 samples, 0 phenotypes, 0 genotypes)
  • Assessment of diagnostic doses for widely used synthetic pyrethroids (Deltamethrin & Permethrin) in an endemic focus of leishmaniasis in Turkey (VBP0000299: details, map, 1 collections, 1 samples, 10 phenotypes, 0 genotypes)
  • Evaluation of resting traps to examine the behaviour and ecology of mosquito vectors in an area of rapidly changing land use in Sabah, Malaysian Borneo (VBP0000300: details, map, 1 collections, 173 samples, 0 phenotypes, 0 genotypes)
  • Insecticide susceptibility status of Anopheles gambiae (s.l.) in South-West Cameroon four years after long-lasting insecticidal net mass distribution (VBP0000301: details, map, 3 collections, 9 samples, 8 phenotypes, 12 genotypes)
  • A new malaria vector mosquito in South Africa (VBP0000302: details, map, 4 collections, 17 samples, 2 phenotypes, 0 genotypes)
  • Veni, vidi, vici: on the origin and expansion of the mosquito Aedes aegypti in Madeira Island (Portugal) (VBP0000303: details, map, 15 collections, 715 samples, 0 phenotypes, 21373 genotypes)
  • Mosquito surveillance in Cass County, North Dakota, and Clay County, Minnesota, USA. 2010 (VBP0000304: details, map, 1600 collections, 6356 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Cass County, North Dakota, and Clay County, Minnesota, USA. 2011 (VBP0000305: details, map, 2147 collections, 7522 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Cass County, North Dakota, and Clay County, Minnesota, USA. 2013 (VBP0000306: details, map, 1812 collections, 6987 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Cass County, North Dakota, and Clay County, Minnesota, USA. 2014 (VBP0000307: details, map, 2710 collections, 8992 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Cass County, North Dakota, and Clay County, Minnesota, USA. 2015 (VBP0000308: details, map, 3180 collections, 11021 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Cass County, North Dakota, and Clay County, Minnesota, USA. 2016 (VBP0000309: details, map, 3039 collections, 11243 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Cass County, North Dakota, and Clay County, Minnesota, USA. 2017 (VBP0000310: details, map, 2770 collections, 8407 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Salt Lake County, Utah, USA. 2013 (VBP0000311: details, map, 676 collections, 2657 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Salt Lake County, Utah, USA. 2014 (VBP0000312: details, map, 1002 collections, 4023 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Salt Lake County, Utah, USA. 2015 (VBP0000313: details, map, 1222 collections, 4875 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Salt Lake County, Utah, USA. 2016 (VBP0000314: details, map, 1227 collections, 4719 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Salt Lake County, Utah, USA. 2017 (VBP0000315: details, map, 1423 collections, 5026 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Lucas County, Ohio, USA. 2014 (VBP0000316: details, map, 1016 collections, 3429 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Lucas County, Ohio, USA. 2015 (VBP0000317: details, map, 1049 collections, 4743 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Lucas County, Ohio, USA. 2016 (VBP0000318: details, map, 1319 collections, 3813 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Lucas County, Ohio, USA. 2017 (VBP0000319: details, map, 1372 collections, 4108 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Cass County, North Dakota, and Clay County, Minnesota, USA. 2012 (VBP0000320: details, map, 1743 collections, 5284 samples, 0 phenotypes, 0 genotypes)

4 projects have been updated (usually to fix minor data inconsistencies):

  • Sequence and structural variation in the genome of the Biomphalaria glabrata embryonic (Bge) cell line (VBP0000226: details, 0 collections, 1 samples, 0 phenotypes, 0 genotypes)
  • Origin of a High-Latitude Population of Aedes aegypti in Washington, DC (VBP0000201: details, map, 23 collections, 643 samples, 0 phenotypes, 6952 genotypes)
  • Larval susceptibility to chemical insecticides of two Aedes aegypti populations (VBP0000084: details, map, 2 collections, 2 samples, 13 phenotypes, 0 genotypes)
  • Malaria control in a tribal area of Central India using existing tools (VBP0000238: details, map, 53 collections, 88 samples, 264 phenotypes, 0 genotypes)

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

    Tutorials

    Follow this link for all the site tutorials, which includes material such as videos with its slides, practice exercises with answer keys, and sample files. Visit our YouTube Channel to watch all our video tutorials. The video slides (including demo outlines), are in our regular tutorial pages. The new and updated tutorials for this release are:

    • We’ve made a new VectorBase Variation Tutorial for SNPs, INDELs, structural variants, and microsatellites. Click here to view the tutorial.
    • We have updated the sample use cases tutorial, which combines the following tools: Search, Genome Browser, BLAST, Comparative Genomics, Clustal, Hmmer, Apollo, Advanced Search, Expression Browser, Population Biology (PopBio), Variation data and BioMart.

      • Click here to view the tutorial


    Future releases

    The next VectorBase release (VB-2018-10) is scheduled for late October.

    Other known issues

      Please report any problems to the helpdesk.

      Release date: 
      Tuesday, August 28, 2018