Release VB-2018-04

We are pleased to announce the April 2018 release of VectorBase (VB-2018-04):
  • Many large (and small) datasets have been added to the Population Biology database, including abundance data from four counties in Florida, additional years of data from Southern Nevada, and entomological monitoring data from Uganda. In total 1.6 million new data records have been added, representing 16 million individual vector specimens.
  • The timelime plots in the PopBio map are more responsive and now show vector abundance averaged over year, month, week or day, as appropriate. Currently our most longitudinal dataset is from Southern Nevada, with nine consecutive years of data.
  • New variation data have been added for
    1. Culex quinquefasciatus (two SNPs implicated in insecticide resistance from the paper by Walter Fabricio Silva Martins et al, "Local selection in the presence of high levels of gene flow: Evidence of heterogeneous insecticide selection pressure across Ugandan Culex quinquefasciatus populations", PLOS, Neglected Tropical Diseases doi.org/10.1371/journal.pntd.0005917).
    2. Biomphalaria glabrata variants derived from the Bge3 cell line from the paper currently in preparation "Sequence and structural variation in the genome of the Biomphalaria glabrata embryonic (Bge) cell line". (Nicolas J. Wheeler, Nathalie Dinguirard, Joshua Marquez, Adrian Gonzalez, Mostafa Zamanian, Timothy P. Yoshino, Maria G. Castillo)
    3. New variation data for the G3 A. gambiae colony provided by Tony Nolan, Imperial College, London.
  • Four new differential expression datasets added, including species Biomphalaria glabrata and Cimex lectularius.
  • New whole genome alignment for Aedes aegypti AaegL5 vs Aedes albopictus, here a sample region in Chromosome 2
  • There are two new video tutorials available, PopBio overview and PopBio insecticide resistance view.
  • Unlike our current practice exercises, we now have a new tutorial integrating most major tools with (four) sample cases. The answer key is provided.
  • The ~80 FAQs have been revised, of these seven questions not relevant or valid any more have been deleted. The FAQs categories updated included General, Site usage, Browser, Expression data, Compara and Community manual annotation with Apollo.

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

Four new experiments have been processed and added to the expression browser:

Population Biology/Insecticide Resistance

41 projects have been added:

  • Comparative evaluation of anopheline sampling methods in three localities in Indonesia (VBP0000237: details, map, 2701 collections, 2701 samples, 0 phenotypes, 0 genotypes)
  • Whole-genome resequencing of 12 female and 12 male Anopheles gambiae G3 strain laboratory colony individuals (VBP0000227: details, 0 collections, 24 samples, 0 phenotypes, 0 genotypes)
  • Seasonal Dynamics of Phlebotomine Sand Fly Species Proven Vectors of Mediterranean Leishmaniasis Caused by Leishmania infantum (VBP0000228: details, map, 207 collections, 6144 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Cyrpus, 2011-2013 (VBP0000229: details, map, 135 collections, 3757 samples, 0 phenotypes, 0 genotypes)
  • Insecticide resistance and target site mutations (G119S ace-1 and L1014F kdr) of Culex pipiens in Morocco (VBP0000230: details, map, 1 collections, 35 samples, 5 phenotypes, 60 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)
  • Development of insecticide resistance in malaria vector Anopheles sinensis populations from Shandong province in China (VBP0000232: details, map, 10 collections, 40 samples, 40 phenotypes, 0 genotypes)
  • Multiple insecticide resistance in Anopheles gambiae from Tanzania: a major concern for malaria vector control (VBP0000233: details, map, 20 collections, 100 samples, 100 phenotypes, 0 genotypes)
  • Reduced Insecticide Susceptibility in Aedes vexans (Diptera: Culicidae) Where Agricultural Pest Management Overlaps With Mosquito Abatement (VBP0000234: details, map, 15 collections, 108 samples, 108 phenotypes, 0 genotypes)
  • Mapping insecticide resistance in Anopheles gambiae (s.l.) from Côte d’Ivoire (VBP0000235: details, map, 47 collections, 269 samples, 197 phenotypes, 144 genotypes)
  • First record of Aedes albopictus in Georgia and updated checklist of reported species (VBP0000236: details, map, 86 collections, 174 samples, 0 phenotypes, 0 genotypes)
  • Malaria control in a tribal area of Central India using existing tools (VBP0000238: details, map, 53 collections, 88 samples, 264 phenotypes, 0 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)
  • Phlebotomine sand flies (Diptera: Psychodidae) in the Greek Aegean Islands: ecological approaches (VBP0000240: details, map, 164 collections, 719 samples, 0 phenotypes, 0 genotypes)
  • Host attraction and biting behaviour of Anopheles mosquitoes in South Halmahera, Indonesia (VBP0000241: details, map, 1235 collections, 1235 samples, 6175 phenotypes, 0 genotypes)
  • Mosquito surveillance in Southern Nevada, USA. 2008 (VBP0000242: details, map, 318 collections, 1092 samples, 2322 phenotypes, 0 genotypes)
  • Mosquito surveillance in Southern Nevada, USA. 2009 (VBP0000243: details, map, 582 collections, 1857 samples, 3825 phenotypes, 0 genotypes)
  • Mosquito surveillance in Southern Nevada, USA. 2010 (VBP0000244: details, map, 697 collections, 2085 samples, 4164 phenotypes, 0 genotypes)
  • Mosquito surveillance in Southern Nevada, USA. 2011 (VBP0000245: details, map, 554 collections, 2020 samples, 4398 phenotypes, 0 genotypes)
  • Mosquito surveillance in Southern Nevada, USA. 2012 (VBP0000246: details, map, 344 collections, 843 samples, 1497 phenotypes, 0 genotypes)
  • Mosquito surveillance in Southern Nevada, USA. 2013 (VBP0000247: details, map, 334 collections, 913 samples, 1737 phenotypes, 0 genotypes)
  • Mosquito surveillance in Hernando County, Florida, USA. 2014 (VBP0000248: details, map, 627 collections, 2367 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Hernando County, Florida, USA. 2015 (VBP0000249: details, map, 464 collections, 2210 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Hernando County, Florida, USA. 2016 (VBP0000250: details, map, 389 collections, 2145 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Hernando County, Florida, USA. 2017 (VBP0000251: details, map, 374 collections, 2134 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance following Hurricane Irma, Hernando County, Florida, USA. 2017 (VBP0000252: details, map, 16 collections, 107 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Manatee County, Florida, USA. 2013 (VBP0000253: details, map, 2516 collections, 15620 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Manatee County, Florida, USA. 2014 (VBP0000254: details, map, 2661 collections, 17382 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Manatee County, Florida, USA. 2015 (VBP0000255: details, map, 2453 collections, 15253 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Manatee County, Florida, USA. 2016 (VBP0000256: details, map, 2458 collections, 15296 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Orange County, Florida, USA. 2012 (VBP0000257: details, map, 2744 collections, 5619 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Orange County, Florida, USA. 2013 (VBP0000258: details, map, 1204 collections, 3289 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Orange County, Florida, USA. 2014 (VBP0000259: details, map, 686 collections, 1939 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Orange County, Florida, USA. 2015 (VBP0000260: details, map, 760 collections, 2325 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Orange County, Florida, USA. 2016 (VBP0000261: details, map, 780 collections, 3079 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Orange County, Florida, USA. 2017 (VBP0000262: details, map, 594 collections, 2125 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 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)
  • Mosquito surveillance in Manatee County, Florida, USA. 2012 (VBP0000266: details, map, 2110 collections, 12938 samples, 0 phenotypes, 0 genotypes)
  • Measures of Malaria Burden after Long-Lasting Insecticidal Net Distribution and Indoor Residual Spraying at Three Sites in Uganda: A Prospective Observational Study (VBP0000267: details, map, 13603 collections, 27896 samples, 6777 phenotypes, 0 genotypes)
8 projects have been updated (usually to fix minor data inconsistencies):
  • Resistance to carbosulfan in Anopheles gambiae from Ivory Coast, based on reduced sensitivity of acetylcholinesterase. (VBP0000114: details, 3 collections, 4 samples, 18 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)
  • 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)
  • 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)
  • 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)
  • Insecticide-Treated Nets and Protection against InsecticideResistant Malaria Vectors in Western Kenya (VBP0000192: details, map, 97 collections, 97 samples, 97 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, 10 genotypes)
  • Local selection in the presence of high levels of gene flow: Evidence of heterogeneous insecticide selection pressure across Ugandan Culex quinquefasciatus populations (VBP0000205: details, map, 5 collections, 542 samples, 0 phenotypes, 9410 genotypes)
These are all available in the PopBio map which now has newly added date and normalized insecticide resistance value search functionality.

Variation Data

Summary of available variation data by organism

Reference speciesAssemblySNP callsIndel calls
Aedes aegypti LiverpoolAaegL3332,4454,081
Aedes aegypti LVP_AGWGAaegL5313,6111,761
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 PESTAgamP459,236,0572,168,425
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 (or youku) Channel to watch all our video tutorials. The video slides (including demo outlines), are in our regular tutorial pages. The new and updated tutorials for this release are:

  • Population Biology or PopBio
  • A new tutorial with use cases that combines the following tools includes: Search, Genome Browser, BLAST, Clustal, Hmmer, Compara, Apollo, BioMart, Advanced Search, Expression Browser and PopBio

Future releases

The next VectorBase release (VB-2018-06) is scheduled for late June.

Other known issues

  • TODO

Please report any problems to the helpdesk.

Release date: 
Tuesday, April 24, 2018