Home » Data » Release Notes » Release VB-2019-04

Release VB-2019-04

Submitted by rwieck on Tue, 2019-04-09 11:15

We are pleased to announce the April 2019 release of VectorBase (VB-2019-04):

New species Leptotrombidium deliense - host vector for scrub typhus. Full details this mite genome are available in the publication "Genomes of trombidid mites reveal novel predicted allergens and laterally transferred genes associated with secondary metabolism." Dong et al, Gigasciene 2018.
In this release there were updates to the gene sets for 4 species based on community annotation ( Aedes aegypti, An. arabiensis, An. farauti, and An. gambiae. ).
New summary tracks have been added in Apollo as a concise compilation of all splice site predictions from our aligned RNA-Seq data. There are two main types of tracks: one "known" (contain splice junctions in accord with the gene model) and several "unknown" (those come with various coverage threshold). Each species also has a merged bigwig file for the coverage.
The variation mart for SNP and indel data will be retired from this release as originally announced in the October 2018 release notes. The variation BioMart has been replaced with the variation search facility which is described in this tutorial.
There is a new view in the PopBio map that visualizes the blood meal hosts of vectors.
Lots of new Population Biology data, including mosquito surveillance data from Iowa going back to the 1970s
The Genotype Explorer application will be retired in the next (June 2019) VectorBase release.
New tutorials includes these six topics: Tour, Aedes & Culex, Genome Browser (includes 6 videos/demos), Anopheles, Query & Browse (Search, BioMart, BLAST, Clustal, Hmmer -includes 6 videos/demos) and Biomphalaria.

Genomes

Released genomes, with gene predictions

Organism	Strain	Assembly	Gene set	Gene Count
Aedes aegypti	Liverpool AGWG	AaegL5	AaegL5.2	19 763
Aedes albopictus	Foshan	AaloF1	AaloF1.2	18 294
Anopheles albimanus	STECLA	AalbS2	AalbS2.6	12 504
Anopheles arabiensis	Dongola	AaraD1	AaraD1.11	13 685
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	AfarF2.6	13 300
Anopheles funestus	FUMOZ	AfunF1	AfunF1.10	13 931
Anopheles gambiae	PEST	AgamP4	AgamP4.12	13 796
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
Leptotrombidium deliense	UoL-UT	LdelU1.	LdelU1.0	14 667
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 resource has been reprocessed/synchronized with the latest gene sets.

Population Biology/Insecticide Resistance

58 projects have been added:

Target-site mutations (AChE-G119S and kdr) in Guangxi Anopheles sinensis populations along the China-Vietnam border (VBP0000441: details, map, 7 collections, 7 samples, 0 phenotypes, 35 genotypes)
Mosquito abundance and viral surveillance, Rhode Island Department of Environmental Management, in Rhode Island, USA, 2018 (VBP0000434: details, map, 413 collections, 2199 samples, 4398 phenotypes, 0 genotypes)
Mosquito surveillance from 2019-01-27 to 2019-03-25 by BG-Counter smart traps owned by Collier Mosquito Control District. (VBP0000442: details, map, 624 collections, 624 samples, 0 phenotypes, 0 genotypes)
Mosquito surveillance from 2019-03-01 to 2019-03-25 by BG-Counter smart traps owned by Biogents AG. (VBP0000443: details, map, 23 collections, 23 samples, 0 phenotypes, 0 genotypes)
Evaluation of toxicity of clothianidin (neonicotinoid) and chlorfenapyr (pyrrole) insecticides and cross-resistance to other public health insecticides in Anopheles arabiensis from Ethiopia (VBP0000448: details, map, 2 collections, 2 samples, 39 phenotypes, 0 genotypes)
Genetic diversity and population structure of the primary malaria vector Anopheles sinensis (Diptera: Culicidae) in China inferred by cox1 gene (VBP0000451: details, map, 20 collections, 452 samples, 0 phenotypes, 452 genotypes)
Phenotypic and genotypic pyrethroid resistance of Aedes albopictus, with focus on the 2017 chikungunya outbreak in Italy (VBP0000445: details, map, 25 collections, 345 samples, 27 phenotypes, 1426 genotypes)
Insecticide resistance and its underlying mechanisms in field populations of Aedes aegypti adults (Diptera: Culicidae) in Singapore (VBP0000446: details, map, 7 collections, 14 samples, 63 phenotypes, 0 genotypes)
Susceptibility status of Aedes aegypti (L.) (Diptera: Culicidae) to temephos in Venezuela (VBP0000447: details, map, 6 collections, 12 samples, 36 phenotypes, 0 genotypes)
Resistance to Malathion and Deltamethrin in Aedes aegypti (Diptera: Culicidae) From Western Venezuela (VBP0000450: details, map, 8 collections, 8 samples, 96 phenotypes, 0 genotypes)
Current insecticide resistance status in Anopheles sacharovi and Anopheles superpictus populations in former malaria endemic areas of Turkey (VBP0000444: details, map, 28 collections, 82 samples, 451 phenotypes, 0 genotypes)
Analyzing mosquito diversity in Pakistan by DNA barcoding. (VBP0000449: details, map, 1583 collections, 1583 samples, 0 phenotypes, 0 genotypes)
Mosquito surveillance, Northwest Mosquito and Vector Control District, in California, USA, 2014 (VBP0000399: details, map, 1022 collections, 5898 samples, 0 phenotypes, 0 genotypes)
Mosquito surveillance, Northwest Mosquito and Vector Control District, in California, USA, 2015 (VBP0000400: details, map, 1357 collections, 7363 samples, 0 phenotypes, 0 genotypes)
Mosquito surveillance, Northwest Mosquito and Vector Control District, in California, USA, 2016 (VBP0000401: details, map, 3847 collections, 17980 samples, 0 phenotypes, 0 genotypes)
Mosquito surveillance, Northwest Mosquito and Vector Control District, in California, USA, 2017 (VBP0000402: details, map, 4039 collections, 19014 samples, 0 phenotypes, 0 genotypes)
Mosquito surveillance, Northwest Mosquito and Vector Control District, in California, USA, 2018 (VBP0000403: details, map, 3193 collections, 12759 samples, 0 phenotypes, 0 genotypes)
Non-mosquito surveillance, Northwest Mosquito and Vector Control District, in California, USA, 2014 (VBP0000404: details, map, 311 collections, 406 samples, 0 phenotypes, 0 genotypes)
Non-mosquito surveillance, Northwest Mosquito and Vector Control District, in California, USA, 2015 (VBP0000405: details, map, 485 collections, 610 samples, 0 phenotypes, 0 genotypes)
Non-mosquito surveillance, Northwest Mosquito and Vector Control District, in California, USA, 2016 (VBP0000406: details, map, 1429 collections, 1898 samples, 0 phenotypes, 0 genotypes)
Non-mosquito surveillance, Northwest Mosquito and Vector Control District, in California, USA, 2018 (VBP0000407: details, map, 739 collections, 1044 samples, 0 phenotypes, 0 genotypes)
Non-mosquito surveillance, Northwest Mosquito and Vector Control District, in California, USA, 2017 (VBP0000408: details, map, 1187 collections, 1639 samples, 0 phenotypes, 0 genotypes)
State-wide mosquito surveillance in Iowa, USA, 1997 (New Jersey light trap) (VBP0000409: details, map, 1357 collections, 7189 samples, 0 phenotypes, 0 genotypes)
State-wide mosquito surveillance in Iowa, USA, 1996 (New Jersey light trap) (VBP0000410: details, map, 1636 collections, 9831 samples, 0 phenotypes, 0 genotypes)
State-wide mosquito surveillance in Iowa, USA, 1995 (New Jersey light trap) (VBP0000411: details, map, 1752 collections, 9851 samples, 0 phenotypes, 0 genotypes)
State-wide mosquito surveillance in Iowa, USA, 1994 (New Jersey light trap) (VBP0000412: details, map, 1808 collections, 9685 samples, 0 phenotypes, 0 genotypes)
State-wide mosquito surveillance in Iowa, USA, 1993 (New Jersey light trap) (VBP0000413: details, map, 1354 collections, 9325 samples, 0 phenotypes, 0 genotypes)
State-wide mosquito surveillance in Iowa, USA, 1992 (New Jersey light trap) (VBP0000414: details, map, 1263 collections, 7393 samples, 0 phenotypes, 0 genotypes)
State-wide mosquito surveillance in Iowa, USA, 1991 (New Jersey light trap) (VBP0000415: details, map, 1368 collections, 7962 samples, 0 phenotypes, 0 genotypes)
State-wide mosquito surveillance in Iowa, USA, 1990 (New Jersey light trap) (VBP0000416: details, map, 1213 collections, 7276 samples, 0 phenotypes, 0 genotypes)
State-wide mosquito surveillance in Iowa, USA, 1989 (New Jersey light trap) (VBP0000417: details, map, 1284 collections, 6707 samples, 0 phenotypes, 0 genotypes)
State-wide mosquito surveillance in Iowa, USA, 1988 (New Jersey light trap) (VBP0000418: details, map, 1027 collections, 4707 samples, 0 phenotypes, 0 genotypes)
State-wide mosquito surveillance in Iowa, USA, 1987 (New Jersey light trap) (VBP0000419: details, map, 1033 collections, 5938 samples, 0 phenotypes, 0 genotypes)
State-wide mosquito surveillance in Iowa, USA, 1986 (New Jersey light trap) (VBP0000420: details, map, 1032 collections, 6474 samples, 0 phenotypes, 0 genotypes)
State-wide mosquito surveillance in Iowa, USA, 1985 (New Jersey light trap) (VBP0000421: details, map, 921 collections, 4878 samples, 0 phenotypes, 0 genotypes)
State-wide mosquito surveillance in Iowa, USA, 1984 (New Jersey light trap) (VBP0000422: details, map, 1718 collections, 11992 samples, 0 phenotypes, 0 genotypes)
State-wide mosquito surveillance in Iowa, USA, 1983 (New Jersey light trap) (VBP0000423: details, map, 1376 collections, 8621 samples, 0 phenotypes, 0 genotypes)
State-wide mosquito surveillance in Iowa, USA, 1982 (New Jersey light trap) (VBP0000424: details, map, 986 collections, 7750 samples, 0 phenotypes, 0 genotypes)
State-wide mosquito surveillance in Iowa, USA, 1981 (New Jersey light trap) (VBP0000425: details, map, 1235 collections, 7883 samples, 0 phenotypes, 0 genotypes)
State-wide mosquito surveillance in Iowa, USA, 1980 (New Jersey light trap) (VBP0000426: details, map, 2100 collections, 14921 samples, 0 phenotypes, 0 genotypes)
State-wide mosquito surveillance in Iowa, USA, 1979 (New Jersey light trap) (VBP0000427: details, map, 1834 collections, 13222 samples, 0 phenotypes, 0 genotypes)
State-wide mosquito surveillance in Iowa, USA, 1978 (New Jersey light trap) (VBP0000428: details, map, 1878 collections, 14355 samples, 0 phenotypes, 0 genotypes)
State-wide mosquito surveillance in Iowa, USA, 1977 (New Jersey light trap) (VBP0000429: details, map, 1938 collections, 15599 samples, 0 phenotypes, 0 genotypes)
State-wide mosquito surveillance in Iowa, USA, 1976 (New Jersey light trap) (VBP0000430: details, map, 1776 collections, 11331 samples, 0 phenotypes, 0 genotypes)
State-wide mosquito surveillance in Iowa, USA, 1975 (New Jersey light trap) (VBP0000431: details, map, 112 collections, 1086 samples, 0 phenotypes, 0 genotypes)
State-wide mosquito surveillance in Iowa, USA, 1970 (New Jersey light trap) (VBP0000432: details, map, 127 collections, 799 samples, 0 phenotypes, 0 genotypes)
State-wide mosquito surveillance in Iowa, USA, 1969 (New Jersey light trap) (VBP0000433: details, map, 107 collections, 679 samples, 0 phenotypes, 0 genotypes)
Mosquito viral surveillance, Northwest Mosquito and Vector Control District, in California, USA, 2014 (VBP0000394: details, map, 175 collections, 231 samples, 693 phenotypes, 0 genotypes)
Mosquito viral surveillance, Northwest Mosquito and Vector Control District, in California, USA, 2015 (VBP0000395: details, map, 321 collections, 413 samples, 1239 phenotypes, 0 genotypes)
Mosquito viral surveillance, Northwest Mosquito and Vector Control District, in California, USA, 2016 (VBP0000396: details, map, 352 collections, 384 samples, 1194 phenotypes, 0 genotypes)
Mosquito viral surveillance, Northwest Mosquito and Vector Control District, in California, USA, 2017 (VBP0000397: details, map, 487 collections, 507 samples, 1520 phenotypes, 0 genotypes)
Mosquito viral surveillance, Northwest Mosquito and Vector Control District, in California, USA, 2018 (VBP0000398: details, map, 249 collections, 259 samples, 777 phenotypes, 0 genotypes)
UK Culicoides surveillance, Pirbright Institute, UK, 2006 (VBP0000435: details, map, 235 collections, 3252 samples, 0 phenotypes, 0 genotypes)
UK Culicoides surveillance, Pirbright Institute, UK, 2007 (VBP0000436: details, map, 355 collections, 4017 samples, 0 phenotypes, 0 genotypes)
UK Culicoides surveillance, Pirbright Institute, UK, 2008 (VBP0000437: details, map, 461 collections, 5168 samples, 0 phenotypes, 0 genotypes)
UK Culicoides surveillance, Pirbright Institute, UK, 2009 (VBP0000438: details, map, 331 collections, 3115 samples, 0 phenotypes, 0 genotypes)
UK Culicoides surveillance, Pirbright Institute, UK, 2010 (VBP0000439: details, map, 311 collections, 3322 samples, 0 phenotypes, 0 genotypes)
UK Culicoides surveillance, Pirbright Institute, UK, 2011 (VBP0000440: details, map, 132 collections, 1206 samples, 0 phenotypes, 0 genotypes)

29 projects have been updated (usually to fix minor data inconsistencies):

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)
Does insecticide resistance contribute to heterogeneities in malaria transmission in The Gambia? (VBP0000174: details, map, 16 collections, 44 samples, 45 phenotypes, 37 genotypes)
Phlebotomine sand flies (Diptera: Psychodidae) in the Greek Aegean Islands: ecological approaches (VBP0000240: details, map, 164 collections, 719 samples, 0 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 by smart traps owned by Collier Mosquito Control District. 2018 (VBP0000344: details, map, 3136 collections, 3133 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 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 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)
Mosquito surveillance, Ada County Weed, Pest, and Mosquito, in Idaho, USA, 2017 (VBP0000385: details, map, 1860 collections, 7961 samples, 0 phenotypes, 0 genotypes)
Mosquito surveillance, Ada County Weed, Pest, and Mosquito, in Idaho, USA, 2018 (VBP0000386: details, map, 2285 collections, 7582 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)
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)
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 Manatee County, Florida, USA. 2014 (VBP0000254: details, map, 2661 collections, 17382 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)
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)
Malathion resistance in mosquitos from Charleston and Georgetown counties of coastal South Carolina (VBP0000094: details, map, 29 collections, 29 samples, 36 phenotypes, 0 genotypes)
Resistance to carbosulfan in Anopheles gambiae from Ivory Coast, based on reduced sensitivity of acetylcholinesterase. (VBP0000114: details, 3 collections, 4 samples, 11 phenotypes, 0 genotypes)
Plasticity of host selection by malaria vectors of Papua New Guinea (VBP0000175: details, map, 2446 collections, 2446 samples, 2536 phenotypes, 0 genotypes)
Transgenic Metarhizium pingshaense synergistically ameliorates pyrethroid-resistance in wild-caught, malaria-vector mosquitoes (VBP0000321: details, map, 2 collections, 570 samples, 0 phenotypes, 1140 genotypes)
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)
Susceptibility profile of Aedes aegypti from Santiago Island, Cabo Verde, to insecticides (VBP0000361: details, map, 3 collections, 3 samples, 16 phenotypes, 0 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)
First detection of a Vssc allele V1016G conferring a high level of insecticide resistance in Aedes albopictus collected from Europe (Italy) and Asia (Vietnam), 2016: a new emerging threat to controlling arboviral diseases (VBP0000370: details, map, 6 collections, 300 samples, 7 phenotypes, 2051 genotypes)

Variation Data

Summary of available variation data by organism

Reference species	Assembly	SNP calls	Indel calls
Aedes aegypti LVP_AGWG	AaegL5	314,633	1,770
Anopheles arabiensis Dongola	AaraD1	10,164,339	1,022,752
Anopheles culicifacies A-37	AculA1	9,154,354	900,063
Anopheles epiroticus Epiroticus2	AepiE1	3,281,528	267,653
Anopheles farauti FAR1	AfarF2	7,226,209	871,433
Anopheles funestus FUMOZ	AfunF1	12,920,105	987,886
Anopheles gambiae PEST	AgamP4	59,236,536	2,168,425
Anopheles melas CM1001059_A	AmelC2	3,677,409	418,730
Anopheles merus MAF	AmerM2	6,053,485	558,680
Anopheles minimus MINIMUS1	AminM1	4,206,083	222,877
Anopheles quadriannulatus SANGWE	AquaS1	10,137,655	931,982
Anopheles sinensis SINENSIS	AsinS2	5,841,551	409,698
Anopheles stephensi SDA-500	AsteS1	5,856,684	574,778
Anopheles stephensi Indian	AsteI2	366,367	0
Biomphalaria glabrata BB02	BglaB1	10,031,395	0
Culex quinquefasciatus Johannesburg	CpipJ2	2	0
Ixodes scapularis Wikel	IscaW1	1,776,352	0

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 and youku channels 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
Aedes & Culex
Genome Browser (includes 6 videos/demos)
Anopheles
Query & Browse (Search, BioMart, BLAST, Clustal, Hmmer -includes 6 videos/demos)
Biomphalaria

Future releases

The next VectorBase release (VB-2019-06) is scheduled for late June.

Other known issues

Please report any problems to the helpdesk.

Release date:

Wednesday, April 24, 2019