Release VB-2019-02

We are pleased to announce the February 2019 release of VectorBase (VB-2019-02):
  • In this release there were updates to the gene sets for 7 species based on community annotation ( An. arabiensis, An. coluzzii, An. funestus, An. gambiae, An. merus, An. quadriannulatus and Stomoxys calcitrans ).
  • HTseq read depth statistics are now generated for all RNAseq alignments and can be accessed via the RNAseq experiment pages in the search facility (see also the RNAseq tutorial).
  • As part of our planning for contract renewal we are discontinuing Apollo patch builds from the February 2019 release. The Apollo system will still be open to the community to make gene model edits, but these alterations will not be committed back into the VectorBase databases until Apollo has been transferred to the new contract holder. We currently anticipate that Apollo patch builds will commence from March 2020.
  • Following the introduction of the variation search facility in August 2018 the current variation mart support will be discontinued from the April 2019 release as noted in the October 2018 release notes.
  • Updates to gene expression metrics as a consequence of the gene set updates for all species
  • 20 years of mosquito surveillance data from Iowa, USA. (1998-2017) Many thanks to Lyric Bartholomay, Ryan Smith, and colleagues for sharing the data.
  • Mosquito surveillance data from Ada County, Idaho (2017-18)
  • The Apollo annotation tool was updated to version 2.2.0
  • PopBio Map bug fixes and improvements such as the Share Link button now capturing optimized colors and plot changes, the plots can now be limited to show the top 14 categories of the data being graphed, and UX/UI improvements
  • The schedule for the 2019 outreach activities is available, and it features a calendar for your convenience. Meetings we plan to attend to host a booth, present a talk and/or poster include AMCA Feb 25-Mar 1, AGS June 12-14, VectorBiTE June 17-22, ISOPS July 15-19 and Mosquito and other vectors July 22-26. A workshop in Guatemala, June 3-5. Private webinars -Virtual lab meetings from Feb 1 to Sep 13. Public webinars - tool/resource specific and species/group specific sessions, each with seven and eight different events respectively from Feb 5 to Sep 10.

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 AaraD1.10 13 816
Anopheles atroparvus EBRO AatrE3 AatrE3.1 14 078
Anopheles christyi ACHKN1017 AchrA1 AchrA1.7 11 185
Anopheles coluzzii Mali-NIH AcolM1 AcolM1.8 14 796
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 gambiae PEST AgamP4 AgamP4.11 13 822
Anopheles maculatus maculatus3 AmacM1 AmacM1.5 15 018
Anopheles melas CM1001059_A AmelC2 AmelC2.6 15 765
Anopheles merus MAF AmerM2 AmerM2.9 13 605
Anopheles minimus MINIMUS1 AminM1 AminM1.8 13 127
Anopheles quadriannulatus SANGWE AquaS1 AquaS1.11 13 934
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 ScalU1.5 16 950

Expression data

No new data has been added, but the expression data has been reprocessed for the updated gene builds. A new expression map has been generated also.

Population Biology/Insecticide Resistance

35 projects have been added:

  • Culex annulirostris (Diptera: Culicidae) Host Feeding Patterns and Japanese Encephalitis Virus Ecology in Northern Australia (VBP0000358: details, map, 5 collections, 5 samples, 50 phenotypes, 0 genotypes)
  • Vector bionomics and malaria transmission in an area of sympatry of An. arabiensis, An. coluzzii and An. gambiae (VBP0000359: details, map, 4 collections, 68 samples, 72 phenotypes, 0 genotypes)
  • First detection of N1575Y mutation in pyrethroid resistant Anopheles gambiae in Southern Côte d’Ivoire (VBP0000360: details, map, 2 collections, 5 samples, 12 phenotypes, 6 genotypes)
  • Susceptibility profile of Aedes aegypti from Santiago Island, Cabo Verde, to insecticides (VBP0000361: details, map, 3 collections, 3 samples, 16 phenotypes, 0 genotypes)
  • Insecticide susceptibility of Aedes albopictus and Ae. aegypti from Brazil and the Swiss-Italian border region. (VBP0000362: details, 1 collections, 1109 samples, 1154 phenotypes, 0 genotypes)
  • Pyrethroids resistance intensity and resistance mechanisms in Anopheles gambiae from malaria vector surveillance sites in Nigeria (VBP0000363: details, map, 6 collections, 18 samples, 61 phenotypes, 33 genotypes)
  • Anopheles species composition and entomological parameters in malaria endemic localities of North West Colombia (VBP0000364: details, map, 6 collections, 25 samples, 0 phenotypes, 0 genotypes)
  • Quantification of permethrin resistance and kdr alleles in Florida strains of Aedes aegypti (L.) and Aedes albopictus (Skuse) (VBP0000365: details, map, 57 collections, 57 samples, 0 phenotypes, 228 genotypes)
  • Regional Comparison of Mosquito Bloodmeals in South Australia: Implications for Ross River Virus Ecology (VBP0000366: details, map, 128 collections, 194 samples, 194 phenotypes, 0 genotypes)
  • Status of insecticide resistance in malaria vectors in Kwale County, Coastal Kenya (VBP0000367: details, map, 3 collections, 39 samples, 18 phenotypes, 4 genotypes)
  • A Statewide Survey of Container Aedes Mosquitoes (Diptera: Culicidae) in North Carolina, 2016: A Multiagency Surveillance Response to Zika Using Ovitraps (VBP0000368: details, map, 3449 collections, 15771 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance from 2018-11-26 to 2018-12-13 by BG-Counter smart traps owned by Biogents AG. (VBP0000373: details, map, 36 collections, 36 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance from 2019-01-09 to 2019-01-24 by BG-Counter smart traps owned by Biogents AG. (VBP0000374: details, map, 16 collections, 16 samples, 0 phenotypes, 0 genotypes)
  • State-wide mosquito surveillance in Iowa, USA, 2017 (New Jersey light trap) (VBP0000369: details, map, 2187 collections, 11100 samples, 0 phenotypes, 0 genotypes)
  • State-wide mosquito surveillance in Iowa, USA, 2016 (New Jersey light trap) (VBP0000371: details, map, 2095 collections, 11284 samples, 0 phenotypes, 0 genotypes)
  • State-wide mosquito surveillance in Iowa, USA, 2015 (New Jersey light trap) (VBP0000372: details, map, 2642 collections, 11958 samples, 0 phenotypes, 0 genotypes)
  • State-wide mosquito surveillance in Iowa, USA, 2012 (New Jersey light trap) (VBP0000377: details, map, 2581 collections, 8332 samples, 0 phenotypes, 0 genotypes)
  • State-wide mosquito surveillance in Iowa, USA, 2011 (New Jersey light trap) (VBP0000378: details, map, 2830 collections, 10671 samples, 0 phenotypes, 0 genotypes)
  • State-wide mosquito surveillance in Iowa, USA, 2010 (New Jersey light trap) (VBP0000379: details, map, 2888 collections, 13310 samples, 0 phenotypes, 0 genotypes)
  • State-wide mosquito surveillance in Iowa, USA, 2009 (New Jersey light trap) (VBP0000380: details, map, 2305 collections, 9774 samples, 0 phenotypes, 0 genotypes)
  • State-wide mosquito surveillance in Iowa, USA, 2008 (New Jersey light trap) (VBP0000381: details, map, 2125 collections, 10893 samples, 0 phenotypes, 0 genotypes)
  • State-wide mosquito surveillance in Iowa, USA, 2007 (New Jersey light trap) (VBP0000382: details, map, 2522 collections, 11837 samples, 0 phenotypes, 0 genotypes)
  • State-wide mosquito surveillance in Iowa, USA, 2006 (New Jersey light trap) (VBP0000383: details, map, 4333 collections, 12684 samples, 0 phenotypes, 0 genotypes)
  • State-wide mosquito surveillance in Iowa, USA, 2005 (New Jersey light trap) (VBP0000384: details, map, 3055 collections, 16562 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance, Ada County Weed, Pest, and Mosquito, in Idaho, USA, 2017 (VBP0000385: details, map, 4439 collections, 13123 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance, Ada County Weed, Pest, and Mosquito, in Idaho, USA, 2018 (VBP0000386: details, map, 3823 collections, 10672 samples, 0 phenotypes, 0 genotypes)
  • State-wide mosquito surveillance in Iowa, USA, 2004 (New Jersey light trap) (VBP0000387: details, map, 3974 collections, 17348 samples, 0 phenotypes, 0 genotypes)
  • State-wide mosquito surveillance in Iowa, USA, 2003 (New Jersey light trap) (VBP0000388: details, map, 3732 collections, 17410 samples, 0 phenotypes, 0 genotypes)
  • State-wide mosquito surveillance in Iowa, USA, 2002 (New Jersey light trap) (VBP0000389: details, map, 2124 collections, 9692 samples, 0 phenotypes, 0 genotypes)
  • State-wide mosquito surveillance in Iowa, USA, 2001 (New Jersey light trap) (VBP0000390: details, map, 1854 collections, 12081 samples, 0 phenotypes, 0 genotypes)
  • State-wide mosquito surveillance in Iowa, USA, 2000 (New Jersey light trap) (VBP0000391: details, map, 1086 collections, 6518 samples, 0 phenotypes, 0 genotypes)
  • State-wide mosquito surveillance in Iowa, USA, 1999 (New Jersey light trap) (VBP0000392: details, map, 1430 collections, 9148 samples, 0 phenotypes, 0 genotypes)
  • State-wide mosquito surveillance in Iowa, USA, 1998 (New Jersey light trap) (VBP0000393: details, map, 1418 collections, 8207 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance from 2019-01-01 to 2019-01-26 by BG-Counter smart traps owned by Collier Mosquito Control District. (VBP0000376: details, map, 205 collections, 205 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance from 2018-11-26 to 2018-12-31 by BG-Counter smart traps owned by Collier Mosquito Control District. (VBP0000375: details, map, 388 collections, 388 samples, 0 phenotypes, 0 genotypes)
33 projects have been updated (usually to fix minor data inconsistencies):
  • Effective population sizes of a major vector of human diseases, Aedes aegypti (VBP0000193: details, map, 29 collections, 1383 samples, 0 phenotypes, 30018 genotypes)
  • Global Genetic Diversity of Aedes aegypti (VBP0000138: details, map, 83 collections, 3708 samples, 0 phenotypes, 88274 genotypes)
  • Multiple introductions of the dengue vector, Aedes aegypti, into California (VBP0000177: details, map, 16 collections, 519 samples, 0 phenotypes, 11015 genotypes)
  • UC Davis/UCLA population dataset (VBP0000005: details, map, 819 collections, 30769 samples, 0 phenotypes, 198812 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)
  • State-wide mosquito surveillance in Iowa, USA. 2013-2014 (VBP0000194: details, map, 7000 collections, 19175 samples, 2680 phenotypes, 0 genotypes)
  • Mosquito surveillance in Lucas County, Ohio, USA. 2014 (VBP0000316: details, map, 1016 collections, 3429 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Salt Lake County, Utah, USA. 2017 (VBP0000315: details, map, 1423 collections, 5026 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)
  • 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, 10170 genotypes)
  • Origin of a High-Latitude Population of Aedes aegypti in Washington, DC (VBP0000201: details, map, 23 collections, 643 samples, 0 phenotypes, 6952 genotypes)
  • Veni, vidi, vici: on the origin and expansion of the mosquito Aedes aegypti in Madeira Island (Portugal) (VBP0000303: details, map, 15 collections, 715 samples, 0 phenotypes, 21373 genotypes)
  • Mosquito surveillance in Cass County, North Dakota, and Clay County, Minnesota, USA. 2010 (VBP0000304: details, map, 1600 collections, 6356 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Cass County, North Dakota, and Clay County, Minnesota, USA. 2011 (VBP0000305: details, map, 2147 collections, 7522 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Cass County, North Dakota, and Clay County, Minnesota, USA. 2013 (VBP0000306: details, map, 1812 collections, 6987 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Cass County, North Dakota, and Clay County, Minnesota, USA. 2014 (VBP0000307: details, map, 2710 collections, 8992 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Cass County, North Dakota, and Clay County, Minnesota, USA. 2015 (VBP0000308: details, map, 3180 collections, 11021 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Cass County, North Dakota, and Clay County, Minnesota, USA. 2016 (VBP0000309: details, map, 3039 collections, 11243 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Cass County, North Dakota, and Clay County, Minnesota, USA. 2017 (VBP0000310: details, map, 2770 collections, 8407 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Salt Lake County, Utah, USA. 2013 (VBP0000311: details, map, 676 collections, 2657 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Salt Lake County, Utah, USA. 2014 (VBP0000312: details, map, 1002 collections, 4023 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Salt Lake County, Utah, USA. 2015 (VBP0000313: details, map, 1222 collections, 4875 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Salt Lake County, Utah, USA. 2016 (VBP0000314: details, map, 1227 collections, 4719 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Lucas County, Ohio, USA. 2015 (VBP0000317: details, map, 1049 collections, 4743 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Lucas County, Ohio, USA. 2016 (VBP0000318: details, map, 1319 collections, 3813 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Lucas County, Ohio, USA. 2017 (VBP0000319: details, map, 1372 collections, 4108 samples, 0 phenotypes, 0 genotypes)
  • Mosquito surveillance in Cass County, North Dakota, and Clay County, Minnesota, USA. 2012 (VBP0000320: details, map, 1743 collections, 5284 samples, 0 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)
  • Malathion resistance in mosquitos from Charleston and Georgetown counties of coastal South Carolina (VBP0000094: details, map, 29 collections, 29 samples, 36 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)
  • Ecological niche partitioning between Anopheles gambiae molecular forms in Cameroon: the ecological side of speciation (VBP0000008: details, map, 4206 collections, 4206 samples, 0 phenotypes, 10797 genotypes)
  • ANVR 1st dataset (VBP0000009: details, map, 228 collections, 228 samples, 456 phenotypes, 0 genotypes)
  • Mosquito surveillance in South Walton County, Florida, USA. 2015 (VBP0000263: details, map, 1954 collections, 7726 samples, 0 phenotypes, 0 genotypes)

Variation Data

Summary of available variation data by organism

Reference speciesAssemblySNP callsIndel calls
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 in our regular tutorial pages. The updated tutorial for this release is:

Additionally, the VectorBase 2019 webinar series slides are also available to you:


Future releases

The next VectorBase release (VB-2019-04) is scheduled for late April.

Other known issues

Please report any problems to the helpdesk.

Release date: 
Tuesday, February 19, 2019