Release VB-2017-04

We are pleased to announce the April 2017 release of VectorBase (VB-2017-04):

• The Aedes albopictus C6/36 cell line assembly (canu_80X_arrow2.2) data are available from the Downloads section
• In this release there have been updates to genes sets for twelve Anopheline species. The latest gene set updates have been derived from community supplied gene annotations for Anopheles arabiensis, Anopheles albimanus, Anopheles darlingi, Anopheles dirus, Anopheles farauti, Anopheles funestus, Anopheles gambiae, Anopheles melas, Anopheles merus, Anopheles minimus, Anopheles quadriannulatus and Anopheles stephensi.
• Microarray probe mappings and variation consequence effects have been updated for all species.
• New ortholog metrics have been added to help with the identification of "high confidence" orthologs. A new FAQ discusses the new metrics, such as the Gene Order Conservation (GOC) score.
• Four new differential expression experiments added.
• Fourteen new population biology datasets added, including sample metadata from the MalariaGen 1000 Anopheles gambiae genomes project, insecticide resistance studies and several large new blood meal species identification studies.
• BLAST has been been updated to allow sorting across all organism hits, by utilizing the expand all and sort all buttons.
• New options for higher e-values were added to BLAST. Previously, our highest e-value allowed was 10. Current options include 100, 1000, 10000 and 100000. You can test this new feature when using protein queries against scaffolds in tBLASTn for the search of (new) highly derived/rapidly evolving genes.
• Three tutorials have been updated for this release: BioMart, BLAST and Web Apollo.
• New page for workshops, meetings, and conferences attended by VectorBase.
• Search page now allows users to search using a file

Genomes

Released genomes, with gene predictions

Organism	Strain	Assembly	Gene set	Gene Count	Browser
Aedes aegypti	Liverpool	AaegL3	AaegL3.4	16 955
Aedes albopictus	Foshan	AaloF1	AaloF1.2	18 294
Anopheles albimanus	STECLA	AalbS2	AalbS2.3	12 500
Anopheles arabiensis	Dongola	AaraD1	AaraD1.6	13 830
Anopheles atroparvus	EBRO	AatrE1	AatrE1.4	14 113
Anopheles christyi	ACHKN1017	AchrA1	AchrA1.4	11 081
Anopheles coluzzii	Mali-NIH	AcolM1	AcolM1.4	14 891
Anopheles culicifacies A	A-37	AculA1	AculA1.4	14 713
Anopheles darlingi	Coari	AdarC3	AdarC3.5	10 958
Anopheles dirus	WRAIR2	AdirW1	AdirW1.5	13 216
Anopheles epiroticus	Epiroticus2	AepiE1	AepiE1.4	12 547
Anopheles farauti	FAR1	AfarF2	AfarF2.3	13 325
Anopheles funestus	FUMOZ	AfunF1	AfunF1.6	13 920
Anopheles gambiae	PEST	AgamP4	AgamP4.6	13 756
Anopheles maculatus	maculatus3	AmacM1	AmacM1.4	15 016
Anopheles melas	CM1001059_A	AmelC2	AmelC2.4	15 726
Anopheles merus	MAF	AmerM2	AmerM2.4	13 664
Anopheles minimus	MINIMUS1	AminM1	AminM1.5	13 078
Anopheles quadriannulatus	SANGWE	AquaS1	AquaS1.6	13 959
Anopheles sinensis	China	AsinC2	AsinC2.2	19 694
Anopheles sinensis	SINENSIS	AsinS2	AsinS2.2	13 170
Anopheles stephensi	Indian	AsteI2	AsteI2.3	12 189
Anopheles stephensi	SDA-500	AsteS1	AsteS1.5	13 601
Biomphalaria glabrata	BB02	BglaB1	BglaB1.5	15 912
Cimex lectularius	Harlan	ClecH1	ClecH1.3	15 292
Culex quinquefasciatus	Johannesburg	CpipJ2	CpipJ2.3	19 796
Glossina austeni	TTRI	GausT1	GausT1.4	20 117
Glossina brevipalpis	IAEA	GbreI1	GbreI1.4	14 972
Glossina fuscipes	IAEA	GfusI1	GfusI1.4	20 514
Glossina morsitans	Yale	GmorY1	GmorY1.6	12 809
Glossina pallidipes	IAEA	GpalI1	GpalI1.4	19 650
Glossina palpalis	IAEA	GpapI1	GpapI1.2	20 526
Ixodes scapularis	Wikel	IscaW1	IscaW1.5	23 340
Lutzomyia longipalpis	Jacobina	LlonJ1	LlonJ1.3	10 513
Musca domestica	Aabys	MdomA1	MdomA1.3	16 135
Pediculus humanus	USDA	PhumU2	PhumU2.2	11 713
Phlebotomus papatasi	Israel	PpapI1	PpapI1.3	11 615
Rhodnius prolixus	CDC	RproC3	RproC3.2	15 741
Sarcoptes scabiei var. canis	Arlian	SscaA1	SscaA1.2	10 797
Stomoxys calcitrans	USDA	ScalU1	ScalU1.2	16 874

Expression data

New experiments processed and added to the expression browser:

• Brugia malayi infection, blood-feeding time-series, Liverpool strain (Choi et al., 2014) Aedes aegypti RNA-seq experiment
• Brugia malayi infection, blood-feeding time-series, RED strain (Choi et al., 2014) Aedes aegypti RNA-seq experiment
• Diapause induction time-series (Poelchau et al., 2013) Aedes albopictus RNA-seq experiment
• Diapause induction and blood feeding (Huang et al., 2015) Aedes albopictus RNA-seq experiment

Population Biology/Insecticide Resistance

14 projects have been added:

• Susceptibility of Anopheles gambiae to insecticides used for malaria vector control in Rwanda (38 samples, 38 collections, 140 phenotypes, 42 genotypes)
• Natural diversity of the malaria vector Anopheles gambiae (765 samples, 765 collections, 0 phenotypes, 7650 genotypes)
• Levels of insecticide resistance to deltamethrin, malathion, and temephos, and associated mechanisms in Aedes aegypti mosquitoes from the Guadeloupe and Saint Martin islands (French West Indies) (21 samples, 19 collections, 40 phenotypes, 24 genotypes)
• Circumsporozoite protein rates, blood-feeding pattern and frequency of knockdown resistance mutations in Anopheles spp. in two ecological zones of Mauritania (17 samples, 17 collections, 12 phenotypes, 12 genotypes)
• Intensive trapping of blood-fed Anopheles darlingi in Amazonian Peru reveals unexpectedly high proportions of avian blood-meals (4417 samples, 37 collections, 0 phenotypes, 0 genotypes)
• WHO cone bio-assays of classical and new-generation long-lasting insecticidal nets call for innovative insecticides targeting the knock-down resistance mechanism in Benin (20 samples, 20 collections, 0 phenotypes, 10 genotypes)
• Evidence of multiple insecticide resistance mechanisms in Anopheles gambiae populations in Bangui, Central African Republic (14 samples, 7 collections, 42 phenotypes, 7 genotypes)
• A Survey of Insecticide Resistance in Aedes albopictus (Diptera: Culicidae) During a 2014 Dengue Fever Outbreak in Guangzhou, China (0 samples, 0 collections, 0 phenotypes, 0 genotypes)
• A significant association between deltamethrin resistance, Plasmodium falciparum infection and the Vgsc-1014S resistance mutation in Anopheles gambiae highlights the epidemiological importance of resistance markers (470 samples, 1 collections, 0 phenotypes, 503 genotypes)
• DDT and pyrethroid resistance status and laboratory evaluation of bio-efficacy of long lasting insecticide treated nets against Culex quinquefasciatus and Culex decens in Ghana (9 samples, 0 collections, 27 phenotypes, 2 genotypes)
• Insecticide susceptibility of Anopheles coluzzii and Anopheles gambiae mosquitoes in Ibadan, South-West Nigeria (14 samples, 14 collections, 13 phenotypes, 8 genotypes)
• Distribution of Voltage-Gated Sodium Channel (Nav) Alleles among the Aedes aegypti Populations In Central Java Province and Its Association with Resistance to Pyrethroid Insecticides (28 samples, 0 collections, 48 phenotypes, 48 genotypes)
• Does insecticide resistance contribute to heterogeneities in malaria transmission in The Gambia? (37 samples, 15 collections, 45 phenotypes, 15 genotypes)
• Plasticity of host selection by malaria vectors of Papua New Guinea (2446 samples, 2446 collections, 2536 phenotypes, 0 genotypes)

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

• Sequencing studies of MR4 derived insect colonies (21 samples, 0 collections, 0 phenotypes, 0 genotypes)
• Contrasting patterns of insecticide resistance and knockdown resistance (kdr) in the dengue vectors Aedes aegypti and Aedes albopictus from Malaysia (48 samples, 24 collections, 101 phenotypes, 48 genotypes)
• Genotyping and permethrin-resistance phenotyping of Anopheles gambiae M and S form mosquitoes from Cameroon, Ghana, Uganda and Guinea-Bissau (1833 samples, 4 collections, 2 phenotypes, 0 genotypes)
• Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes (98 samples, 98 collections, 0 phenotypes, 0 genotypes)
• Dynamics of pyrethroid resistance in malaria vectors in southern Benin following a large scale implementation of vector control interventions (184 samples, 184 collections, 59 phenotypes, 112 genotypes)
• Discovery of Point Mutations in the Voltage-Gated Sodium Channel from African Aedes aegypti Populations: Potential Phylogenetic Reasons for Gene Introgression
  (19 samples, 14 collections, 16 phenotypes, 20 genotypes)
• Composition and genetics of malaria vector populations in the Central African Republic (37 samples, 15 collections, 140 phenotypes, 0 genotypes)
• Insecticide susceptibility of Anopheles stephensi to DDT and current insecticides in an elimination area in Iran. (11 samples, 1 collections, 11 phenotypes, 0 genotypes)

In this release, the population biology project pages have been updated. The old Google Maps, bar charts and dot plots have been removed, and replaced with a link to the PopBio Map. In future releases we aim to improve the charting functionality of the PopBio Map, which currently produces basic plots in insecticide resistance view.

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 new YouTube Channel to watch all our video tutorials, we plan to add one for each release. The video slides (including demo outlines), are in our regular tutorial pages. The new and updated tutorials for this release are:

• BioMart
• BLAST
• Web Apollo

Known issues

• The project contact Matthew B. Thomas (Center for Infectious Disease Dynamics and Department of Entomology, Pennsylvania State University, University Park, PA, 16802, USA) has been omitted from PopBio project VBP0000162. This will be rectified as soon as possible.

Future releases

The next VectorBase release (VB-2017-06) is scheduled for late June.

Please report any problems to the helpdesk.