Release VB-2017-08

We are pleased to announce the August 2017 release of VectorBase (VB-2017-08):
  • The gene set for Biomphalaria glabrata has been updated to the NCBI Biomphalaria glabrata Annotation Release 100, and combined with RNA gene models based on alignment to Rfam (v12.1) covariance models. Both the previous and latest gene sets for Biomphalaria glabrata are available in the Apollo editor for community annotation projects to work with.
  • In this release most of the variation databases have been updated to use VCF data storage for genotypes. VectorBase users should not notice any difference in performance, but if you do encounter any issues please contact the helpdesk.
  • The current Anopheles albimanus INSDC assembly update resulted in a minor change to the scaffold names and INSDC assembly id. These changes are not yet synchronised with this release of VectorBase, and will be resolved in October 2017 release.
  • Two large population biology datasets have been updated with new data. The President's Malaria Initiative insecticide resistance dataset now has 4,618 phenotypes (2,926 previously). The UC Davis/UCLA Anopheles gambiae complex population genetics dataset now contains 30,769 individual mosquito samples (13,654 previously).
  • Three differential expression RNA-seq datasets have been added to the expression browser.
  • Five insecticide resistance studies have been added to the population biology resource.
  • The PopBio Map now has animated aggregation and disaggregation of markers (easier to see than explain!)
  • The Data Files now allows for multiple files to be downloaded simultaneously.
  • Filter widgets can be added to other parts of the site other than the Search page. The InterPro pages displayed through the Search Result Details module and the Supplementary Dataset pages currently use this new feature.
  • The page for data submission has been updated.
  • There is a new FAQ (Which are the gene biotype definitions?) and updates to two related ones (What the gene set counts mean? and How are RNA genes annotated?). New Glossary entries include the 16 gene biotype terms.
  • The BioMart and Search tutorials have been updated.
  • From September to November this year (2017), we are going to provide 1-hour private lab meetings/webinars to interested groups. If you would like to nominate your lab please send us a message to with details about what your lab does (250 words maximum) and the specific questions you want to be addressed by VectorBase during the meeting.


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 BglaB1.6 31 985
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:

Population Biology/Insecticide Resistance

Five new projects have been added:

  • Knockdown resistance (kdr) of the voltage-gated sodium channel gene of Aedes aegypti population in Denpasar, Bali, Indonesia (VBP0000189: details, map, 6 collections, 6 samples, 0 phenotypes, 18 genotypes)
  • Insecticide resistance in malaria vectors along the Thailand-Myanmar border (VBP0000190: details, map, 76 collections, 76 samples, 78 phenotypes, 0 genotypes)
  • Species Identification and Resistance Status of Anopheles gambiae s.l. (Diptera: Culicidae) Mosquitoes in Guinea (VBP0000188: details, map, 19 collections, 19 samples, 8 phenotypes, 12 genotypes)
  • Insecticide-Treated Nets and Protection against Insecticide Resistant Malaria Vectors in Western Kenya (VBP0000192: details, map, 97 collections, 97 samples, 97 phenotypes, 0 genotypes)
  • First report of the East African kdr mutation in an Anopheles gambiae mosquito in Côte d’Ivoire (VBP0000191: details, map, 1 collections, 4 samples, 4 phenotypes, 0 genotypes)
Two projects have had major updates. Both projects have approximately double the amount of data compared to before.
  • President's Malaria Initiative (PMI) insecticide susceptibility data (VBP0000123: details, map, 4688 collections, 4688 samples, 4618 phenotypes, 31 genotypes)
  • UC Davis/UCLA population dataset (VBP0000005: details, map, 819 collections, 30769 samples, 0 phenotypes, 198812 genotypes)
One project has had some minor updates to fix inconsistencies:
  • 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, map, 2141 collections, 2141 samples, 1341 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


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 and youku Channels 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/or updated tutorials for this release are:

Future releases

The next VectorBase release (VB-2017-10) is scheduled for late October.

Other known issues

  • A problem was encountered with the generation of the dN/dS ratios in the gene BioMart for this release. The current values are incorrect and will be recalculated for all organisms for the October 2017 release
  • Some of the new samples added in the update to VBP0000005 (UCLA/UC Davis "PopI" population genetics dataset) are also present in other projects already in VectorBase (for example VBP0000006). We will remove the redundancy for the next release.

Please report any problems to the helpdesk.

Release date: 
Tuesday, August 29, 2017