Release VB-2018-10

• In this release there were updates to the gene sets for 24 species based on community annotation ( Anopheles albimanus, An. arabiensis, An. christyi, An. coluzzii, An. culicifacies, An. darlingi, An. dirus, An. epiroticus, An. farauti, An. funestus, An. gambiae, An. melas, An. merus, An. minimus, An. quadriannulatus, An. sinensis (Sinensis strain), An. stephensi (SDA-500 strain), Glossina austeni, G. brevipalpis, G. fuscipes, G. pallidipes, G. palpalis, Lutzomyia longipalpis and Phlebotomus papatasi ).
• New variation data for Anopheles gambiae populations from around Lake Victoria, Uganda as described in the publication "Reduced-representation sequencing identifies small effective population sizes of Anopheles gambiae in the north-western Lake Victoria basin, Uganda." by Wiltshire et al. (2018)
• 3 RNA-Seq new track hubs for Aedes aegypti related to Zika and Dengue viruses:
  • Zika & Dengue virus infections (Anglero-rodriguez et al., Front Microbiol. 2017)
  • DENV1 and DENV3 infections (Suzuki et al., PLoS Negl Trop Dis., 2017)
  • Blood meals infected with Dengue virus 1 (Raquin et al., PLoS Negl Trop Dis. , 2017)
• The VectorBase variation BioMart instance is now scheduled to be retired after the April 2019 VectorBase release. The variation BioMart has been replaced with the new variation search facility which is described in this tutorial. If the retirement of the variation BioMart is likely to cause you any problems please contact us via the helpdesk.
• Lots of new PopBio data has been added, and previously existing abundance data has been updated with information about attractants used in the traps. PopBio projects now have tags and data usage license information which can be used in site search and the map.
• The PopBio map legend and data coloring behaviour has been changed to dynamically reflect the data currently visible
• New Tour video tutorial and new PopBio map sample queries.
• The schedule of the upcoming outreach activities, for the end of this year 2018, is posted in this page. These activities include public and private webinars and workshops. We will also be attending two scientific meetings (ASTMH/TropMed & ESA), come to our posters and talks, or stop by our exhibit booths for a personalized help desk appointments.

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

New experiments processed and added to the expression browser:

• Exposure to Niclosamide (Zhang et al., 2015) Biomphalaria glabrata microarray experiment
• Ixodes ricinus salivary glands (Perner et al., 2018) Ixodes scapularis RNA-seq experiment
• Blood meals infected with Dengue virus 1 (Raquin et al., 2017) Aedes aegypti RNA-seq experiment
• Dengue virus infections (Suzuki et al., 2017) Aedes aegypti RNA-seq experiment
• Zika and Dengue virus infections (Anglero-Rodriguez et al., 2017) Aedes aegypti RNA-seq experiment

Population Biology

24 projects have been added:

• Transgenic Metarhizium pingshaense synergistically ameliorates pyrethroid-resistance in wild-caught, malaria-vector mosquitoes (VBP0000321: details, map, 2 collections, 570 samples, 0 phenotypes, 1140 genotypes)
• Impact of partially and fully closed eaves on house entry rates by mosquitoes (VBP0000322: details, map, 4 collections, 5000 samples, 0 phenotypes, 0 genotypes)
• Primary malaria vector An. darlingi larvae in a high transmission fish farming area in Amazonian Brazil (VBP0000323: details, map, 337 collections, 4044 samples, 0 phenotypes, 0 genotypes)
• Uneven malaria transmission in geographically distinct districts of Bobo-Dioulasso, Burkina Faso (VBP0000324: details, map, 4 collections, 22 samples, 10 phenotypes, 0 genotypes)
• Pyrethroid resistance in the major malaria vector Anopheles arabiensis in Nouakchott, Mauritania (VBP0000325: details, map, 2 collections, 2 samples, 8 phenotypes, 0 genotypes)
• Emergence of knock-down resistance in the Anopheles gambiae complex in the Upper River Region, The Gambia, and its relationship with malaria infection in children (VBP0000326: details, map, 2 collections, 8 samples, 0 phenotypes, 24 genotypes)
• Insecticide resistance, associated mechanisms and fitness aspects in two Brazilian Stegomyia aegypti (= Aedes aegypti) populations (VBP0000327: details, map, 4 collections, 4 samples, 14 phenotypes, 0 genotypes)
• Change in Anopheles richness and composition in response to artificial flooding during the creation of the Jirau hydroelectric dam in Porto Velho, Brazil (VBP0000328: details, map, 247 collections, 6347 samples, 0 phenotypes, 0 genotypes)
• Barcoding blood meals: New vertebrate-specific primer sets for assigning taxonomic identities to host DNA from mosquito blood meals (VBP0000329: details, map, 1 collections, 63 samples, 60 phenotypes, 0 genotypes)
• Mosquito surveillance in Marion County, Indiana, USA. 2008 (VBP0000330: details, map, 1502 collections, 5912 samples, 0 phenotypes, 0 genotypes)
• Mosquito surveillance in Marion County, Indiana, USA. 2009 (VBP0000331: details, map, 1701 collections, 6796 samples, 0 phenotypes, 0 genotypes)
• Mosquito surveillance in Marion County, Indiana, USA. 2010 (VBP0000332: details, map, 1712 collections, 7314 samples, 0 phenotypes, 0 genotypes)
• Mosquito surveillance in Marion County, Indiana, USA. 2011 (VBP0000333: details, map, 1999 collections, 7021 samples, 0 phenotypes, 0 genotypes)
• Mosquito surveillance in Marion County, Indiana, USA. 2012 (VBP0000334: details, map, 2016 collections, 7316 samples, 0 phenotypes, 0 genotypes)
• Mosquito surveillance in Marion County, Indiana, USA. 2013 (VBP0000335: details, map, 2020 collections, 8075 samples, 0 phenotypes, 0 genotypes)
• Mosquito surveillance in Marion County, Indiana, USA. 2014 (VBP0000336: details, map, 2080 collections, 8047 samples, 0 phenotypes, 0 genotypes)
• Mosquito surveillance in Marion County, Indiana, USA. 2015 (VBP0000337: details, map, 2060 collections, 9647 samples, 0 phenotypes, 0 genotypes)
• Mosquito surveillance in Marion County, Indiana, USA. 2016 (VBP0000338: details, map, 1999 collections, 9431 samples, 0 phenotypes, 0 genotypes)
• Mosquito surveillance in Marion County, Indiana, USA. 2017 (VBP0000339: details, map, 2040 collections, 8992 samples, 0 phenotypes, 0 genotypes)
• Mosquito surveillance in Marion County, Indiana, USA. 2018 (VBP0000340: details, map, 1260 collections, 4518 samples, 0 phenotypes, 0 genotypes)
• Mosquito surveillance by smart traps owned by Biogents AG. 2017 (VBP0000341: details, map, 347 collections, 347 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)
• Mosquito surveillance by smart traps owned by Collier Mosquito Control District. 2017 (VBP0000343: details, map, 477 collections, 477 samples, 0 phenotypes, 0 genotypes)
• Mosquito surveillance by smart traps owned by Collier Mosquito Control District. 2018 (VBP0000344: details, map, 3136 collections, 3136 samples, 0 phenotypes, 0 genotypes)

• Adaptive divergence between incipient species of Anopheles gambiae increases resistance to Plasmodium (VBP0000007: details, map, 9 collections, 97 samples, 0 phenotypes, 0 genotypes)
• Investigation of genetic diversity and phylogeography of wild tick populations in North America. (VBP0000120: details, map, 72 collections, 82 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)
• Global Genetic Diversity of Aedes aegypti. (VBP0000138: details, map, 83 collections, 3708 samples, 0 phenotypes, 88274 genotypes)
• Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes (VBP0000119: details, map, 98 collections, 98 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)
• 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)
• Effective population sizes of a major vector of human diseases, Aedes aegypti (VBP0000193: details, map, 29 collections, 1383 samples, 0 phenotypes, 30018 genotypes)
• Mosquito surveillance in Orange County, Florida, USA. 2017 (VBP0000262: details, map, 594 collections, 2125 samples, 0 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)
• Natural diversity of the malaria vector Anopheles gambiae (VBP0000163: details, map, 765 collections, 765 samples, 0 phenotypes, 7650 genotypes)
• Mosquito surveillance in Southern Nevada, USA. 2014 (VBP0000215: details, map, 625 collections, 1905 samples, 3840 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)
• 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. 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 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)
• Mosquito surveillance in Manatee County, Florida, USA. 2013 (VBP0000253: details, map, 2516 collections, 15620 samples, 0 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)
• 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 Anastasia, Saint Johns County, Florida, USA. 2006 (VBP0000280: details, map, 1854 collections, 3247 samples, 0 phenotypes, 0 genotypes)
• Mosquito surveillance in Anastasia, Saint Johns County, Florida, USA. 2007 (VBP0000281: details, map, 1650 collections, 4505 samples, 0 phenotypes, 0 genotypes)
• Mosquito surveillance in Anastasia, Saint Johns County, Florida, USA. 2008 (VBP0000282: details, map, 1436 collections, 5257 samples, 0 phenotypes, 0 genotypes)
• Mosquito surveillance in Anastasia, Saint Johns County, Florida, USA. 2009 (VBP0000283: details, map, 1407 collections, 5497 samples, 0 phenotypes, 0 genotypes)
• Mosquito surveillance in Anastasia, Saint Johns County, Florida, USA. 2010 (VBP0000284: details, map, 1212 collections, 3242 samples, 0 phenotypes, 0 genotypes)
• Mosquito surveillance in Anastasia, Saint Johns County, Florida, USA. 2011 (VBP0000285: details, map, 1326 collections, 3246 samples, 0 phenotypes, 0 genotypes)
• Mosquito surveillance in Anastasia, Saint Johns County, Florida, USA. 2012 (VBP0000286: details, map, 270 collections, 842 samples, 0 phenotypes, 0 genotypes)
• Mosquito surveillance in Anastasia, Saint Johns County, Florida, USA. 2013 (VBP0000287: details, map, 1107 collections, 3718 samples, 0 phenotypes, 0 genotypes)
• Mosquito surveillance in Anastasia, Saint Johns County, Florida, USA. 2014 (VBP0000288: details, map, 843 collections, 3188 samples, 0 phenotypes, 0 genotypes)
• Mosquito surveillance in Anastasia, Saint Johns County, Florida, USA. 2015 (VBP0000289: details, map, 951 collections, 3276 samples, 0 phenotypes, 0 genotypes)
• Mosquito surveillance in Anastasia, Saint Johns County, Florida, USA. 2016 (VBP0000290: details, map, 624 collections, 1780 samples, 0 phenotypes, 0 genotypes)
• Mosquito surveillance in Anastasia (BG-Sentinel), Saint Johns County, Florida, USA. 2014 (VBP0000291: details, map, 136 collections, 618 samples, 0 phenotypes, 0 genotypes)
• Mosquito surveillance in Anastasia (BG-Sentinel), Saint Johns County, Florida, USA. 2015 (VBP0000292: details, map, 101 collections, 355 samples, 0 phenotypes, 0 genotypes)
• Mosquito surveillance in Anastasia (BG-Sentinel), Saint Johns County, Florida, USA. 2017 (VBP0000293: details, map, 159 collections, 652 samples, 0 phenotypes, 0 genotypes)
• Mosquito surveillance in Anastasia (BG-Sentinel), Saint Johns County, Florida, USA. 2016 (VBP0000294: details, map, 240 collections, 739 samples, 0 phenotypes, 0 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)
• Reduced-representation sequencing identifies small effective population sizes of Anopheles gambiae in the north-western Lake Victoria basin, Uganda (VBP0000212: details, map, 9 collections, 96 samples, 0 phenotypes, 91 genotypes)
• Aedes aegypti in the Black Sea (VBP0000269: details, map, 5 collections, 124 samples, 0 phenotypes, 2848 genotypes)
• Population structure of a vector of human diseases: Aedes aegypti in its ancestral range, Africa (VBP0000295: details, map, 38 collections, 315 samples, 0 phenotypes, 0 genotypes)
• Sequence and structural variation in the genome of the Biomphalaria glabrata embryonic (Bge) cell line (VBP0000226: details, 0 collections, 1 samples, 0 phenotypes, 0 genotypes)

Variation Data

Summary of available variation data by organism

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 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:

• Tour
• Population Biology

Future releases

The next VectorBase release (VB-2018-12) is scheduled for late December.

Other known issues

Please report any problems to the helpdesk.