Release VB-2018-02

We are pleased to announce the February 2018 release of VectorBase (VB-2018-02):

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 AatrE2 AatrE2.1 14 080
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 AmerM2.6 13 676
Anopheles minimus MINIMUS1 AminM1 AminM1.6 13 091
Anopheles quadriannulatus SANGWE AquaS1 AquaS1.8 13 945
Anopheles sinensis SINENSIS AsinS2 AsinS2.4 13 181
Anopheles sinensis China AsinC2 AsinC2.2 19 694
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 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:

The expression maps have also been updated for this release.

Population Biology/Insecticide Resistance

13 projects have been added:

  • Insecticide resistance to permethrin and malathion and associated mechanisms in Aedes aegypti mosquitoes from St. Andrew Jamaica (VBP0000216: details, map, 5 collections, 50 samples, 40 phenotypes, 20 genotypes)
  • Polymorphisms in voltage-gated sodium channel gene and susceptibility of Aedes albopictus to insecticides in three districts of northern West Bengal, India (VBP0000217: details, map, 7 collections, 26 samples, 30 phenotypes, 26 genotypes)
  • Insecticide susceptibility status of invasive Aedes albopictus across dengue endemic districts of Odisha, India. (VBP0000218: details, map, 10 collections, 70 samples, 40 phenotypes, 66 genotypes)
  • First evidence of resistance to pyrethroid insecticides in Italian Aedes albopictus populations after 26 years since invasion (VBP0000219: details, map, 11 collections, 57 samples, 41 phenotypes, 0 genotypes)
  • Insecticide susceptibility of Aedes aegypti and Aedes albopictus in Central Africa (VBP0000220: details, map, 6 collections, 43 samples, 60 phenotypes, 0 genotypes)
  • Composition of Anopheles mosquitoes, their blood-meal hosts, and Plasmodium falciparum infection rates in three islands with disparate bed net coverage in Lake Victoria, Kenya (VBP0000221: details, map, 11 collections, 11 samples, 132 phenotypes, 0 genotypes)
  • Distribution and abundance of key vectors of Rift Valley fever and other arboviruses in two ecologically distinct counties in Kenya (VBP0000222: details, map, 14 collections, 280 samples, 0 phenotypes, 0 genotypes)
  • Increasing insecticide resistance in Anopheles funestus and Anopheles arabiensis in Malawi, 2011–2015 (VBP0000223: details, map, 103 collections, 202 samples, 202 phenotypes, 0 genotypes)
  • Preliminary survey on Anopheles species distribution in Botswana shows the presence of Anopheles gambiae and Anopheles funestus complexes (VBP0000224: details, map, 26 collections, 404 samples, 416 phenotypes, 0 genotypes)
  • Mosquito surveillance in Southern Nevada, USA. 2016 (VBP0000213: details, map, 930 collections, 2751 samples, 5463 phenotypes, 0 genotypes)
  • Mosquito surveillance in Southern Nevada, USA. 2015 (VBP0000214: details, map, 745 collections, 2272 samples, 4581 phenotypes, 0 genotypes)
  • Mosquito surveillance in Southern Nevada, USA. 2014 (VBP0000215: details, map, 625 collections, 1905 samples, 3840 phenotypes, 0 genotypes)
  • Knockdown Resistance (kdr) Mutations in Indian Anopheles stephensi (Diptera: Culicidae) Populations (VBP0000225: details, map, 9 collections, 9 samples, 8 phenotypes, 21 genotypes)
13 projects have been updated (usually to fix minor data inconsistencies):
  • Comparative analysis of response to selection with three insecticides in the dengue mosquito Aedes aegypti using mRNA sequencing. (VBP0000121: details, 0 collections, 4 samples, 0 phenotypes, 0 genotypes)
  • A multipurpose high throughput SNP chip for the dengue and yellow fever mosquito, Aedes aegypti (VBP0000122: details, map, 160 collections, 160 samples, 0 phenotypes, 0 genotypes)
  • Probing functional polymorphisms in the dengue vector, Aedes aegypti (VBP0000015: details, 0 collections, 3 samples, 0 phenotypes, 0 genotypes)
  • UC Davis/UCLA population dataset (VBP0000005: details, map, 819 collections, 30769 samples, 0 phenotypes, 198812 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)
  • 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)
  • Origin of a High-Latitude Population of Aedes aegypti in Washington, DC (VBP0000201: details, map, 7 collections, 292 samples, 0 phenotypes, 6952 genotypes)
  • Insecticide-Treated Nets and Protection against InsecticideResistant Malaria Vectors in Western Kenya (VBP0000192: details, map, 97 collections, 97 samples, 97 phenotypes, 0 genotypes)
  • Multiple mechanisms of resistance to pyrethroids in Anopheles gambiae s.l populations in Niger (VBP0000196: details, map, 7 collections, 63 samples, 52 phenotypes, 14 genotypes)
  • Insecticide resistance status of malaria vectors in Lao PDR (VBP0000210: details, map, 133 collections, 250 samples, 285 phenotypes, 84 genotypes)
  • Natural diversity of the malaria vector Anopheles gambiae (VBP0000163: details, map, 765 collections, 765 samples, 0 phenotypes, 7650 genotypes)
  • 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)

Variation Data

Summary of available variation data by organism

Reference speciesSNP calls (million)Indel calls (million)Last dataset updateLast variation effect update
Aedes aegypti 0.29 0.004 2017-12 2017-12
Anopheles arabiensis 10.2 0.98 2014-10 2018-02
Anopheles culicifacies 9.15 0.88 2014-10 2017-12
Anopheles epiroticus 3.28 0.25 2014-10 2017-12
Anopheles farauti 6.5 0.75 2015-062017-12
Anopheles funestus 12.9 0.47 2014-102018-02
Anopheles gambiae 51.2 14.9 2018-022018-02
Anopheles melas 3.7 0.41 2015-062017-12
Anopheles merus 6.1 0.53 2015-062018-02
Anopheles minimus 4.21 0.22 2014-10 2017-12
Anopheles quadriannulatus 10.1 0.89 2014-102018-02
Anopheles sinensis 5.84 0.41 2015-06 2017-12
Anopheles stephensi SDA-500 5.8 0.57 2014-10 2017-12
Anopheles stephensi Indian 0.37 2014-10 2017-12
Ixodes scapularis 1.78 2015-02 2017-12

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-2018-04) is scheduled for late April.

Other known issues

Please report any problems to the helpdesk.

Release date: 
Wednesday, February 21, 2018