Release VB-2017-10

We are pleased to announce the October 2017 release of VectorBase (VB-2017-10):

Genomes

Released genomes, with gene predictions

Organism Strain Assembly Gene set Gene Count Browser
Aedes aegypti Liverpool AaegL3 AaegL3.5 16 958
Aedes albopictus Foshan AaloF1 AaloF1.2 18 294
Anopheles albimanus STECLA AalbS2 AalbS2.4 12 507
Anopheles arabiensis Dongola AaraD1 AaraD1.7 13 862
Anopheles atroparvus EBRO AatrE1 AatrE1.6 14 080
Anopheles christyi ACHKN1017 AchrA1 AchrA1.6 11 150
Anopheles coluzzii Mali-NIH AcolM1 AcolM1.5 14 887
Anopheles culicifacies A A-37 AculA1 AculA1.5 14 714
Anopheles darlingi Coari AdarC3 AdarC3.6 10 963
Anopheles dirus WRAIR2 AdirW1 AdirW1.6 13 240
Anopheles epiroticus Epiroticus2 AepiE1 AepiE1.6 12 262
Anopheles farauti FAR1 AfarF2 AfarF2.4 13 325
Anopheles funestus FUMOZ AfunF1 AfunF1.7 13 920
Anopheles gambiae PEST AgamP4 AgamP4.8 13 769
Anopheles maculatus maculatus3 AmacM1 AmacM1.5 15 018
Anopheles melas CM1001059_A AmelC2 AmelC2.5 15 753
Anopheles merus MAF AmerM2 AmerM2.5 13 694
Anopheles minimus MINIMUS1 AminM1 AminM1.6 13 091
Anopheles quadriannulatus SANGWE AquaS1 AquaS1.7 13 950
Anopheles sinensis China AsinC2 AsinC2.2 19 694
Anopheles sinensis SINENSIS AsinS2 AsinS2.4 13 181
Anopheles stephensi SDA-500 AsteS1 AsteS1.6 13 614
Anopheles stephensi Indian AsteI2 AsteI2.3 12 189
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 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 PhumU2.3 11 711
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 ScalU1.2 16 874

Expression data

Four new experiments from three publications were processed and added to the expression browser:

Please note that two further species datasets from the Papa et al. 2017 paper will be made available in the next release.

Population Biology/Insecticide Resistance

Ten projects have been added:

  • State-wide mosquito surveillance in Iowa, USA. 2013-2014 (VBP0000194: details, map, 7000 collections, 19175 samples, 2680 phenotypes, 0 genotypes)
  • Insecticide resistance is mediated by multiple mechanisms in recently introduced Aedes aegypti from Madeira Island (Portugal) (VBP0000195: details, map, 16 collections, 16 samples, 8 phenotypes, 16 genotypes)
  • Multiple mechanisms of resistance to pyrethroids in Anopheles gambiae s.l populations in Niger (VBP0000196: details, map, 7 collections, 63 samples, 52 phenotypes, 7 genotypes)
  • Evaluation of piperonyl butoxide in enhancing the efcacy of pyrethroid insecticides against resistant Anopheles gambiae s.l. in Ghana (VBP0000197: details, map, 40 collections, 80 samples, 78 phenotypes, 0 genotypes)
  • Habitat productivity and pyrethroid susceptibility status of Aedes aegypti mosquitoes in Dar es Salaam, Tanzania (VBP0000198: details, map, 6 collections, 144 samples, 144 phenotypes, 0 genotypes)
  • Susceptibility to insecticides and resistance mechanisms in Aedes aegypti from the Colombian Caribbean Region. (VBP0000199: details, map, 9 collections, 81 samples, 81 phenotypes, 0 genotypes)
  • Pyrethroid susceptibility of malaria vectors in four Districts of western Kenya (VBP0000200: details, map, 111 collections, 111 samples, 111 phenotypes, 0 genotypes)
  • Tracking the return of Aedes aegypti to Brazil, the major vector of the dengue, chikungunya and Zika viruses (VBP0000176: details, map, 30 collections, 1032 samples, 0 phenotypes, 24566 genotypes)
  • Multiple introductions of the dengue vector, Aedes aegypti, into California (VBP0000177: details, map, 16 collections, 519 samples, 0 phenotypes, 11015 genotypes)
  • Effective population sizes of a major vector of human diseases, Aedes aegypti (VBP0000193: details, map, 29 collections, 1383 samples, 0 phenotypes, 30018 genotypes)
Two projects have been updated to fix minor data inconsistencies:
  • Genotyping and permethrin-resistance phenotyping of Anopheles gambiae M and S form mosquitoes from Cameroon, Ghana, Uganda and Guinea-Bissau (VBP0000004: details, map, 4 collections, 1833 samples, 2 phenotypes, 0 genotypes)
  • Identifying genomic changes associated with insecticide resistance in the dengue mosquito Aedes aegypti by deep targeted sequencing (VBP0000125: details, 8 collections, 14 samples, 0 phenotypes, 0 genotypes)

Variation Data

Summary of available variation data by organism

Reference speciesSNP calls (million)Indel calls (million)Last dataset updateLast variation effect updatemean SIFT per transcript
Aedes aegypti 0.33 0.004 2016-02 2017-102.0
Anopheles arabiensis 10.2 0.98 2014-10 2017-1010.6
Anopheles culicifacies 9.15 0.88 2014-10 2017-109.3
Anopheles epiroticus 3.28 0.25 2014-10 2017-103.6
Anopheles farauti 6.5 0.75 2015-062017-108.4
Anopheles funestus 12.9 0.47 2014-102017-1015.2
Anopheles gambiae 7.3 1.3 2016-022017-106.8
Anopheles melas 3.7 0.41 2015-062017-103.3
Anopheles merus 6.1 0.53 2015-062017-105.4
Anopheles minimus 4.21 0.22 2014-10 2017-104.2
Anopheles quadriannulatus 10.1 0.89 2014-102017-109.9
Anopheles sinensis 5.84 0.41 2015-06 2017-104.5
Anopheles stephensi SDA-500 5.8 0.57 2014-10 2017-100.4
Anopheles stephensi Indian 0.37 2014-10 2017-105.0
Ixodes scapularis 1.78 2015-02 2017-100.8

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. The video slides (including demo outlines), are in our regular tutorial pages.


Future releases

The next VectorBase release (VB-2017-12) is scheduled for middle December.

Other known issues

  • DONE: The gene expression BioMart database will be updated a few days after the release date. Apologies for any inconvenience.
  • The activation of variation tracks in the genome browser from PopBio application links do not currently work, but manual configuration of variation tracks from the within the genome browser still work as normal.

Please report any problems to the helpdesk.

Release date: 
Wednesday, October 25, 2017