Release VB-2017-06

We are pleased to announce the June 2017 release of VectorBase (VB-2017-06):
  • Differential RNA-seq expression data added from four publications, including a study comparing Anopheles merus and An. coluzzii transcriptional responses to salinity. There is now differential expression data available for ten species.
  • Ten new population biology datasets are available, including larval habitat monitoring for Culex, Anopheles and Aedes in Chennai, India
  • In this release there were updates to the gene sets for 12 species based on community annotation, and a minor gene set update for Anopheles gambiae. The full list of species with updated gene sets in this release is Anopheles atroparvus, Anopheles christyi, Anopheles epiroticus, Anopheles gambiae, Anopheles sinensis, Glossina austeni, Glossina brevipalpis, Glossina fuscipes, Glossina morsitans, Glossina pallidipes, Glossina palpalis, Lutzomyia longipalpis and Phlebotomus papatasi.
  • Protein alignments for all species with updated gene models in this release have been regenerated. These are all-vs-all alignments between the species, which can be viewed as a track in the Genome Browser and Apollo.
  • The VectorBase REST API allowing programmatic access to data is now available for public use
  • A new beta release application - Genotype Explorer - is now available for people to try out. This application can act as a multi species viewer for genetic variation, and allows VCF file export of selected genomic regions and viewing of variants in the context of protein domains and orthologous genes. This application can be used in conjunction with the existing Sample Explorer tool for a subset of VectorBase species which will be expanded in future release releases.
  • The names for the Ixodes scapularis samples from Massachusetts (8 samples) and Wisconsin (12 samples) have been corrected to reflect the values in the BioSample database.
  • Protein domains for annotated transcriptomes have been updated to InterPro version 63.
  • In this release we have standardised on the Ensembl mart view display formats. This has resulted in some minor alterations to the mart interfaces which should not affect any functionality. If any problems are encountered please contact us.
  • We have also improved our Export Results and Export Sequences functionality. Now logged in users will be able to download an unlimited number of search results and sequences. Export Results and Export Sequences will now send the download to a background job and it will be available in the user's profile page under the Export category.
  • We have improved the functionality offered by Search. In order to not restrict our users in what they can search, we have added File Search to our search interface. To use it, click the Switch Search Type text and it will allow you to upload a file with search terms up to 5 KB in size.
  • There are tutorials and practice exercises (with answer key) for the recently launched Sample Explorer and for the new Genotype Explorer. The Apollo and Genome Browser tutorials have also been updated.

Genomes

Released genomes, with gene predictions

Organism Strain Assembly Gene set Gene Count Browser
Aedes aegypti Liverpool AaegL3 AaegL3.4 16 955
Aedes albopictus Foshan AaloF1 AaloF1.2 18 294
Anopheles albimanus STECLA AalbS2 AalbS2.3 12 500
Anopheles arabiensis Dongola AaraD1 AaraD1.6 13 830
Anopheles atroparvus EBRO AatrE1 AatrE1.5 14 073
Anopheles christyi ACHKN1017 AchrA1 AchrA1.5 11 145
Anopheles coluzzii Mali-NIH AcolM1 AcolM1.4 14 891
Anopheles culicifacies A A-37 AculA1 AculA1.4 14 713
Anopheles darlingi Coari AdarC3 AdarC3.5 10 958
Anopheles dirus WRAIR2 AdirW1 AdirW1.5 13 216
Anopheles epiroticus Epiroticus2 AepiE1 AepiE1.5 12 261
Anopheles farauti FAR1 AfarF2 AfarF2.3 13 325
Anopheles funestus FUMOZ AfunF1 AfunF1.6 13 920
Anopheles gambiae PEST AgamP4 AgamP4.7 13 763
Anopheles maculatus maculatus3 AmacM1 AmacM1.4 15 016
Anopheles melas CM1001059_A AmelC2 AmelC2.4 15 726
Anopheles merus MAF AmerM2 AmerM2.4 13 664
Anopheles minimus MINIMUS1 AminM1 AminM1.5 13 078
Anopheles quadriannulatus SANGWE AquaS1 AquaS1.6 13 959
Anopheles sinensis China AsinC2 AsinC2.2 19 694
Anopheles sinensis SINENSIS AsinS2 AsinS2.3 13 177
Anopheles stephensi Indian AsteI2 AsteI2.3 12 189
Anopheles stephensi SDA-500 AsteS1 AsteS1.5 13 601
Biomphalaria glabrata BB02 BglaB1 BglaB1.5 15 912
Cimex lectularius Harlan ClecH1 ClecH1.3 15 292
Culex quinquefasciatus Johannesburg CpipJ2 CpipJ2.3 19 796
Glossina austeni TTRI GausT1 GausT1.5 20 101
Glossina brevipalpis IAEA GbreI1 GbreI1.5 14 987
Glossina fuscipes IAEA GfusI1 GfusI1.5 20 517
Glossina morsitans Yale GmorY1 GmorY1.7 12 850
Glossina pallidipes IAEA GpalI1 GpalI1.5 19 665
Glossina palpalis IAEA GpapI1 GpapI1.3 20 540
Ixodes scapularis Wikel IscaW1 IscaW1.5 23 340
Lutzomyia longipalpis Jacobina LlonJ1 LlonJ1.4 10 650
Musca domestica Aabys MdomA1 MdomA1.3 16 135
Pediculus humanus USDA PhumU2 PhumU2.2 11 713
Phlebotomus papatasi Israel PpapI1 PpapI1.4 11 660
Rhodnius prolixus CDC RproC3 RproC3.2 15 741
Sarcoptes scabiei var. canis Arlian SscaA1 SscaA1.2 10 797
Stomoxys calcitrans USDA ScalU1 ScalU1.2 16 874

Expression data

New experiments processed and added to the expression browser:

This release we are not updating the Expression Maps for Anopheles gambiae and Aedes aegypti. We are reducing the update frequency to approximately twice a year until further notice. If there is a major gene set update or addition of new expression data, we will make additional updates. The maps should still be perfectly usable even if a few months out of date.

Population Biology/Insecticide Resistance

10 projects have been added:

  • Susceptibility profile and metabolic mechanisms involved in Aedes aegypti and Aedes albopictus resistant to DDT and deltamethrin in the Central African Republic (VBP0000178: details, map, 24 collections, 26 samples, 69 phenotypes, 5 genotypes)
  • Blood-feeding patterns of native mosquitoes and insights into their potential role as pathogen vectors in the Thames estuary region of the United Kingdom (VBP0000179: details, 2141 collections, 2141 samples, 1341 phenotypes, 0 genotypes)
  • Evidence of a multiple insecticide resistance in the malaria vector Anopheles funestus in South West Nigeria (VBP0000180: details, map, 1 collections, 55 samples, 49 phenotypes, 15 genotypes)
  • Combined target site (kdr) mutations play a primary role in highly pyrethroid resistant phenotypes of Aedes aegypti from Saudi Arabia (VBP0000181: details, map, 34 collections, 34 samples, 32 phenotypes, 45 genotypes)
  • Overhead tank is the potential breeding habitat of Anopheles stephensi in an urban transmission setting of Chennai, India (VBP0000182: details, map, 827 collections, 6306 samples, 0 phenotypes, 0 genotypes)
  • Presence of susceptible wild strains of Anopheles gambiae in a large industrial palm farm located in Aboisso, South-Eastern of Côte d’Ivoire (VBP0000183: details, map, 3 collections, 3 samples, 6 phenotypes, 4 genotypes)
  • Insecticide resistance patterns in Uganda and the effect of indoor residual spraying with bendiocarb on kdr L1014S frequencies in Anopheles gambiae s.s. (VBP0000184: details, map, 34 collections, 34 samples, 29 phenotypes, 18 genotypes)
  • Novel mutations on the ace-1 gene of the malaria vector Anopheles albimanus provide evidence for balancing selection in an area of high insecticide resistance in Peru (VBP0000185: details, map, 3 collections, 3 samples, 0 phenotypes, 12 genotypes)
  • Insecticide resistance in malaria vector mosquitoes in a gold mining town in Ghana and implications for malaria control (VBP0000186: details, map, 9 collections, 9 samples, 18 phenotypes, 0 genotypes)
  • Genome analysis of a major urban malaria vector mosquito, Anopheles stephensi (VBP0000187: details, 0 collections, 1 samples, 0 phenotypes, 0 genotypes)
3 projects have been updated (usually to fix minor data inconsistencies):
  • Investigation of genetic diversity and phylogeography of wild tick populations in North America. (VBP0000120: details, map, 72 collections, 82 samples, 0 phenotypes, 0 genotypes)
  • Insecticide susceptibility and vector status of natural populations of Anopheles arabiensis from Sudan (VBP0000154: details, map, 13 collections, 13 samples, 52 phenotypes, 0 genotypes)
  • Vectorial status and insecticide resistance of Anopheles funestus from a sugar estate in southern Mozambique (VBP0000146: details, map, 1 collections, 5 samples, 7 phenotypes, 0 genotypes)

Variation Data

Summary of available variation data by organism

Reference speciesSNP calls (million)Indel calls (million)Last dataset updateLast 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 2015-062015-06
Anopheles funestus 12.9 0.47 2014-102015-06
Anopheles gambiae 7.3 1.3 2016-022016-02
Anopheles melas 3.7 0.41 2015-062015-06
Anopheles merus 6.1 0.53 2015-062015-06
Anopheles minimus 4.21 0.22 2014-10 2015-08
Anopheles quadriannulatus 10.1 0.89 2014-102015-08
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 new YouTube Channel to watch all our video tutorials, we plan to add one for each release. The video slides (including demo outlines), are in our regular tutorial pages. The new and updated tutorials for this release are:


Future releases

The next VectorBase release (VB-2017-08) is scheduled for late August.

Other known issues

  • Many of the population biology projects added this release need their "study design types" correcting. Project VBP0000180 uses an erroneous genotype ontology term so its genotypes are not searchable and downloadble. Project VBP0000179 has some missing data, including latitude and longitude coordinates (all points are from this location (51.377445°N, 0.78406°E). All these issues will be fixed in the August release.

Please report any problems to the helpdesk.

Release date: 
Tuesday, June 27, 2017