Release VB-2018-12

We are pleased to announce the December 2018 release of VectorBase (VB-2018-12):
  • As noted in the VectorBase June 2018 release notes support for the Aedes aegypti L3 genome assembly will be discontinued after this release. The Ensembl Genomes site continues to host the old VectorBase AaegL3 browser and BioMart instance, but these resources will also be discontinued by Ensembl in early 2019. VectorBase continues to provide a number of other resources to help with the transition between assemblies and older gene sets.

    https:// www.vectorbase.org/downloads?field_organism_taxonomy_tid%5B%5D=3...

    • Aedes-aegypti-Liverpool_MAPPINGS_AaegL3.5-AaegL5.1.txt - Stable gene ID mapping between genesets AaegL3.5 and AaegL5.1
    • Aedes-aegypti-Liverpool_MAPPINGS_AaegL3.3-AaegL3.4.txt - Stable gene ID mapping between genesets AaegL3.3 and AaegL3.4 (RNA gene update)
    • Aedes-aegypti-Liverpool_MODIFICATIONS_AaegL2.2-AaegL3.1-ncRNA.txt - Liverpool strain gene prediction stable identifier mapping for ncRNA from the AaegL2.2 to AaegL3.1 geneset
  • Dynamic legend in the PopBio map: updates as you move around the map, and you can optimize the data colors on-the-fly
  • First biochemical insecticide resistance assay data added to the database
  • Major remedial work done on the older insecticide resistance data in PopBio. Mostly the fixing of missing units, concentrations and durations.
  • "Barcoded" samples now part of PopBio. The sequences are stored and will be available through CSV downloads in a future release.
  • The schedule for 2019 outreach activities is open. Please send a messages to info@vectorbase.org if you would like to host a workshop (click here for information). Registration is open for virtual lab meetings, these webinars have no cost. More meetings and events will be added during the year.
  • A new version of the VectorBase workshop handout is available here, the page includes a the student copy and the answer key. Email the help desk for questions or feedback.
  • An updated version of the Apollo FAQ 'Automatic emails explained' is available.
  • The gene manual edition tool we use, Apollo, will stop receiving annotations for at least six months next year. This means that your new gene or edit submissions will be incorporated as part of VectorBase official gene sets, probably only once in 2019 and will start again with more regular updates in 2020. While we post the official schedule, we strongly encourage you to complete your Apollo work as soon as possible.
  • The VectorBase team will be celebrating the holidays with their families from December 22nd, 2018 to January 6th, 2019. Please continue to send inquiries to the help desk (info@vectorbase.org) if needed, but note a formal response will likely come in the new year when we return to our offices. We wish you all a happy and safe holiday season!

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 AalbS2.6 12 504
Anopheles arabiensis Dongola AaraD1 AaraD1.9 13 845
Anopheles atroparvus EBRO AatrE3 AatrE3.1 14 078
Anopheles christyi ACHKN1017 AchrA1 AchrA1.7 11 185
Anopheles coluzzii Mali-NIH AcolM1 AcolM1.7 14 851
Anopheles culicifacies A A-37 AculA1 AculA1.6 14 727
Anopheles darlingi Coari AdarC3 AdarC3.8 11 002
Anopheles dirus WRAIR2 AdirW1 AdirW1.8 13 251
Anopheles epiroticus Epiroticus2 AepiE1 AepiE1.7 12 286
Anopheles farauti FAR1 AfarF2 AfarF2.5 13 332
Anopheles funestus FUMOZ AfunF1 AfunF1.9 13 927
Anopheles gambiae PEST AgamP4 AgamP4.10 13 839
Anopheles maculatus maculatus3 AmacM1 AmacM1.5 15 018
Anopheles melas CM1001059_A AmelC2 AmelC2.6 15 765
Anopheles merus MAF AmerM2 AmerM2.8 13 638
Anopheles minimus MINIMUS1 AminM1 AminM1.8 13 127
Anopheles quadriannulatus SANGWE AquaS1 AquaS1.10 13 950
Anopheles sinensis SINENSIS AsinS2 AsinS2.5 13 204
Anopheles sinensis China AsinC2 AsinC2.2 19 694
Anopheles stephensi Indian AsteI2 AsteI2.3 12 189
Anopheles stephensi SDA-500 AsteS1 AsteS1.7 13 615
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 GausT1.7 20 099
Glossina brevipalpis IAEA GbreI1 GbreI1.7 14 991
Glossina fuscipes IAEA GfusI1 GfusI1.7 20 502
Glossina morsitans Yale GmorY1 GmorY1.9 12 869
Glossina pallidipes IAEA GpalI1 GpalI1.7 19 639
Glossina palpalis IAEA GpapI1 GpapI1.4 20 536
Ixodes scapularis Wikel IscaW1 IscaW1.6 23 340
Lutzomyia longipalpis Jacobina LlonJ1 LlonJ1.5 10 760
Musca domestica Aabys MdomA1 MdomA1.3 16 135
Pediculus humanus USDA PhumU2 PhumU2.4 11 712
Phlebotomus papatasi Israel PpapI1 PpapI1.5 11 821
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

No new data this release. However, the expression data download files now no longer apply the "median subtraction" normalisation step. This was confusing users and resulted in an irreversible loss of information in the downloaded files. If users wish to subtract the median per gene/experiment combination, they can do this themselves. Please ask for further information on how to do this.

Population Biology/Insecticide Resistance

11 projects have been added:

  • Mosquito surveillance from 2018-10-10 to 2018-11-25 by BG-Counter smart traps owned by Collier Mosquito Control District. (VBP0000347: details, map, 507 collections, 507 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance from 2018-10-10 to 2018-11-25 by BG-Counter smart traps owned by Biogents AG (VBP0000348: details, map, 101 collections, 101 samples, 0 phenotypes, 0 genotypes)
  • DNA Barcodes Can Distinguish Species of Indian Mosquitoes (Diptera: Culicidae) (VBP0000349: details, map, 111 collections, 111 samples, 0 phenotypes, 111 genotypes)
  • First report of Anopheles stephensi from Djibouti, Horn of Africa (VBP0000350: details, map, 2 collections, 2 samples, 0 phenotypes, 2 genotypes)
  • Identification of Belgian mosquito species (Diptera: Culicidae) by DNA barcoding (VBP0000352: details, map, 260 collections, 260 samples, 0 phenotypes, 260 genotypes)
  • Molecular identification of mosquitoes (Diptera: Culicidae) in southeastern Australia (VBP0000353: details, map, 113 collections, 113 samples, 0 phenotypes, 113 genotypes)
  • Distribution pattern and genetic structure of Aedes zammitii (Diptera: Culicidae) along the Mediterranean and Aegean coasts of Turkey (VBP0000354: details, map, 116 collections, 116 samples, 0 phenotypes, 116 genotypes)
  • DNA barcode sequences used to identify Aedes (Stegomyia) albopictus (Diptera: Culicidae) in La Tebaida (Quindío, Colombia) (VBP0000355: details, map, 18 collections, 18 samples, 0 phenotypes, 18 genotypes)
  • A Novel Sampling Method to Measure Socioeconomic Drivers of Aedes albopictus Distribution in Mecklenburg County, North Carolina (VBP0000356: details, map, 1079 collections, 1079 samples, 0 phenotypes, 0 genotypes)
  • Socioeconomic Determinants of Aedes Mosquito Distribution in the Urban Environment in Panama. (VBP0000357: details, map, 1908 collections, 1908 samples, 0 phenotypes, 0 genotypes)
  • Identification of Swedish mosquitoes based on molecular barcoding of the COI gene (VBP0000351: details, map, 14 collections, 14 samples, 0 phenotypes, 14 genotypes)
38 projects have been updated (usually to fix minor data inconsistencies):
  • Aedes aegypti resistance to temefos in counties of Ceara State (VBP0000082: details, map, 4 collections, 4 samples, 9 phenotypes, 0 genotypes)
  • Mosquito surveillance by smart traps owned by Collier Mosquito Control District. 2018 (VBP0000344: details, map, 3136 collections, 3134 samples, 0 phenotypes, 0 genotypes)
  • ANVR 1st dataset (VBP0000009: details, map, 228 collections, 228 samples, 456 phenotypes, 0 genotypes)
  • Insecticide Susceptible/Resistance Status in Aedes (Stegomyia) aegypti and Aedes (Stegomyia) albopictus (Diptera: Culicidae) in Thailand During 2003-2005 (VBP0000050: details, map, 34 collections, 34 samples, 174 phenotypes, 0 genotypes)
  • Trend of Temephos Resistance in Aedes (Stegomyia) Mosquitoes in Thailand During 2003-2005 (VBP0000051: details, map, 2 collections, 2 samples, 2 phenotypes, 0 genotypes)
  • Potential for organophosphate resistance in Aedes aegypti (Diptera, Culicidae) in the Caribbean area and neighbouring countries (VBP0000097: details, 0 collections, 31 samples, 105 phenotypes, 0 genotypes)
  • Monitoring of resistance to the pyrethroid cypermethrin in Brazilian Aedes aegypti (Diptera : Culicidae) populations collected between 2001 and 2003 (VBP0000098: details, map, 25 collections, 25 samples, 25 phenotypes, 0 genotypes)
  • The kdr pyrethroid resistance gene in Anopheles gambiae: tests of non-pyrethroid insecticides and a new detection method for the gene. (VBP0000104: details, 5 collections, 5 samples, 4 phenotypes, 0 genotypes)
  • Comparison of deltamethrin tablet formulation with liquid deltamethrin and permethrin for bednet treatment in The Gambia. (VBP0000107: details, 1 collections, 1 samples, 3 phenotypes, 0 genotypes)
  • Insecticide-treated plastic tarpaulins for control of malaria vectors in refugee camps. (VBP0000108: details, 1 collections, 1 samples, 9 phenotypes, 0 genotypes)
  • Comparative insecticidal power of three pyrethroids on netting. (VBP0000109: details, 2 collections, 2 samples, 12 phenotypes, 0 genotypes)
  • Biochemical studies on malathion resistance in Anopheles arabiensis from Sudan. (VBP0000111: details, 12 collections, 12 samples, 60 phenotypes, 0 genotypes)
  • Combined pyrethroid and carbamate 'two-in-one' treated mosquito nets: field efficacy against pyrethroid-resistant Anopheles gambiae and Culex quinquefasciatus. (VBP0000113: details, 2 collections, 2 samples, 4 phenotypes, 0 genotypes)
  • Experimental hut comparisons of nets treated with carbamate or pyrethroid insecticides, washed or unwashed, against pyrethroid-resistant mosquitoes. (VBP0000115: details, 4 collections, 4 samples, 20 phenotypes, 0 genotypes)
  • Mixed-function oxidases and esterases associated with cross-resistance between DDT and lambda-cyhalothrin in Anopheles darlingi Root 1926 populations from Colombia (VBP0000118: details, map, 6 collections, 6 samples, 66 phenotypes, 0 genotypes)
  • President's Malaria Initiative (PMI) insecticide susceptibility data (VBP0000123: details, map, 4688 collections, 4688 samples, 4430 phenotypes, 31 genotypes)
  • Insecticide resistance status of Aedes aegypti (L.) from Colombia (VBP0000126: details, map, 12 collections, 12 samples, 192 phenotypes, 0 genotypes)
  • Insecticide resistance status in Culex quinquefasciatus in Benin (VBP0000133: details, map, 4 collections, 4 samples, 16 phenotypes, 8 genotypes)
  • Contrasting patterns of insecticide resistance and knockdown resistance (kdr) in the dengue vectors Aedes aegypti and Aedes albopictus from Malaysia (VBP0000135: details, map, 24 collections, 48 samples, 101 phenotypes, 96 genotypes)
  • When intensity of deltamethrin resistance in Anopheles gambiae s.l. leads to loss of Long Lasting Insecticidal Nets bio-efficacy: a case study in north Cameroon (VBP0000141: details, map, 12 collections, 12 samples, 14 phenotypes, 9 genotypes)
  • Multiple-Insecticide Resistance and Classic Gene Mutations to Japanese Encephalitis Vector Culex tritaeniorhynchus from China (VBP0000145: details, map, 12 collections, 12 samples, 41 phenotypes, 24 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)
  • Exposure to deltamethrin affects development of Plasmodium falciparum inside wild pyrethroid resistant Anopheles gambiae s.s. mosquitoes in Uganda (VBP0000161: details, map, 1 collections, 2 samples, 0 phenotypes, 4 genotypes)
  • Susceptibility to insecticides and resistance mechanisms in Aedes aegypti from the Colombian Caribbean Region. (VBP0000199: details, map, 9 collections, 9 samples, 117 phenotypes, 0 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, map, 2141 collections, 2141 samples, 1341 phenotypes, 0 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)
  • Evidence for multiple-insecticide resistance in urban Aedes albopictus populations in southern China (VBP0000231: details, map, 7 collections, 62 samples, 48 phenotypes, 42 genotypes)
  • First data on resistance to pyrethroids in wild populations of Aedes albopictus from Spain (VBP0000239: details, map, 4 collections, 4 samples, 24 phenotypes, 0 genotypes)
  • Resting and feeding preferences of Anopheles stephensi in an urban setting, perennial for malaria (VBP0000277: details, map, 2 collections, 9 samples, 14 phenotypes, 0 genotypes)
  • Mosquito surveillance in South Walton County, Florida, USA. 2016 (VBP0000264: details, map, 2196 collections, 8784 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in South Walton County, Florida, USA. 2017 (VBP0000265: details, map, 1946 collections, 8516 samples, 0 phenotypes, 0 genotypes)
  • Monitoring resistance to insecticides in Aedes aegypti populations from Brazil (VBP0000268: details, map, 369 collections, 677 samples, 4286 phenotypes, 0 genotypes)
  • Mosquito surveillance in Anastasia, Saint Johns County, Florida, USA. 2004 (VBP0000278: details, map, 2370 collections, 6033 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Anastasia, Saint Johns County, Florida, USA. 2005 (VBP0000279: details, map, 2034 collections, 6365 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in South Walton County, Florida, USA. 2015 (VBP0000263: details, map, 1954 collections, 7726 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance by smart traps owned by Biogents AG. 2018 (VBP0000342: details, map, 822 collections, 822 samples, 0 phenotypes, 0 genotypes)
  • Insecticide resistance, associated mechanisms and fitness aspects in two Brazilian Stegomyia aegypti (= Aedes aegypti) populations (VBP0000327: details, map, 8 collections, 8 samples, 38 phenotypes, 0 genotypes)

Variation Data

Summary of available variation data by organism

Reference speciesAssemblySNP callsIndel calls
Aedes aegypti LiverpoolAaegL3332,4454,081
Aedes aegypti LVP_AGWGAaegL5314,6331,761
Anopheles arabiensis DongolaAaraD110,164,3391,022,752
Anopheles culicifacies A-37AculA19,154,354900,063
Anopheles epiroticus Epiroticus2AepiE13,281,528267,653
Anopheles farauti FAR1AfarF27,226,209871,433
Anopheles funestus FUMOZAfunF112,920,105987,886
Anopheles gambiae PESTAgamP459,236,5362,168,425
Anopheles melas CM1001059_AAmelC23,677,409418,730
Anopheles merus MAFAmerM26,053,485558,680
Anopheles minimus MINIMUS1AminM14,206,083222,877
Anopheles quadriannulatus SANGWEAquaS110,137,655931,982
Anopheles sinensis SINENSISAsinS25,841,551409,698
Anopheles stephensi SDA-500AsteS15,856,684574,778
Anopheles stephensi IndianAsteI2366,3670
Biomphalaria glabrata BB02BglaB110,031,3950
Culex quinquefasciatus JohannesburgCpipJ220
Ixodes scapularis WikelIscaW11,776,3520

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 and youku channels to watch all our video tutorials. The video slides (including demo outlines) are available both in pdf and Google slides format. The updated tutorial for this release is:


Future releases

The next VectorBase release (VB-2019-02) is scheduled for late February.

Other known issues

Please report any problems to the helpdesk.

Release date: 
Wednesday, December 12, 2018