Release VB-2017-12

We are pleased to announce the December 2017 release of VectorBase (VB-2017-12):
  • Aedes aegypti AaegL5 assembly update
    • In this release the old Aedes aegypti AaegL3 assembly has been retired and has been replaced by the latest AaegL5 assembly from the Aedes aegypt Genome Working group. All future annotation and updates at VectorBase will be made on the new AaegL5 assembly.
    • A completely new gene set has been generated for the AaegL5 assembly and is available as the NCBI Aedes aegypti annotation release 101.
    • The NCBI release 101 annotation has been used in this release of VectorBase, and old VectorBase gene ids have been mapped to the new gene set to help users transfer their work to the assembly. The mapping of some of the more complicated gene split and merge events is still ongoing and updates will be made in future releases of VectorBase
    • The AaegL3 assembly is no longer supported in the VectorBase BioMart, search, and Apollo gene annotation applications. A 'frozen' version of the data will continue to be made available via the genome browser, and VectorBase is assisting with the transfer of current AaegL3 based Apollo annotations to the new reference assembly. A new version of the Apollo gene editing application using the AaegL5 assembly will be made available as rapidly as possible.
    • Both Aedes aegypti assemblies used the Liverpool strain for genome sequencing, but to accomodate potential strain specific variation between laboratories these are now differentiated by the use of the suffixes LVP (old AaegL3 assembly) and LVPAGWG (new AaegL5 assembly).
    • Old bookmarks made to the Aedes_aegypti AaegL3 assembly will automatically try to resolve against the new assembly, but may fail if a gene or transcript no longer exists in the new assembly. To resolve this issue add the _lvp or _lvpagwg strain names into the URL to connect to the desired assembly. e.g.
    • RNAseq, expression microarray probes, and SNP variation data have been remapped from AaegL3 to AaegL5 where possible. Not all features could be successfully remapped and there will have been a drop in the overall number of variants mapped, as well as alterations to the derived gene expression profiles. Copy Number Variants (CNV) on the AaegL3 assembly have not been transferred as many of these regions were based on repetitive gene families which have undergone split/merge events on the new assembly.
  • Anopheles atroparvus AatrE2 assembly update
    • A new assembly and gene set have been created for Anopheles atroparvus based on the paper "Partial-arm translocations in evolution of malaria mosquitoes revealed by high- coverage physical mapping of the Anopheles atroparvus genome" (Sharakov et al, BMC Genomics, manuscript submitted).
    • The AatrE2 assembly is a rescaffolding of the sequence of the previous AatrE1 assembly; this has lead to aleration to the genomic feature coordinates, but there have been no changes to the underlying sequences or gene content.
  • The Anopheles gambiae variation database has been updated and variants from dbSNP that had no linked genotype data have been removed. Variants calls for non An. gambiae colonies that were aligned to the An. gambiae PEST sequence have also removed. These two revisions have lead to an ~2% drop in the total number of SNP variants for An. gambiae.
  • We have introduced a new Export feature, called Export STRUCTURE, to enhance Search functionality, for which the exported CSV file can be used with the STRUCTURE software. This can be done through the renovated Export (button) in the Search page where Export Download, Sequence, and STRUCTURE are available in the popup window. Please note that one needs to first select Population Biology (Domain) and Sample genotype (Sub-domain) from the Filter Results in order to activate Export STRUCTURE function (button).
  • The Tools page has been updated to include resources within the tools. We invite you to take a look, most are not new but you may have not noticed them before. One of these is 'Find a Data Display'.
  • Use 'Find a Data Display' to choose a gene, region or variant and then browse for relevant visualizations that include many different types of figures and tables. You can use these visualizations in your presentation, thesis or publication. Contact us if you need help using this resource or have doubts about how to cite the visualizations.
  • Three new differential expression experiments have been added to the expression browser, including the first expression data in VectorBase for Glossina and all Aedes aegypti datasets have been remapped for the new AaegL5 assembly.
  • New RNAseq expression data have been added for Glossina morsitans.
  • Ten new insecticide resistance projects have been added to PopBio and a beta/prototype genotype view is available for testing. This shows allele frequencies for commonly assayed variant loci such as kdr and Ace1.
  • The schedule for outreach activities in the first semester of 2018 is available now, including open registration for the next VectorBase workshop and webinars.

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 AalbS2.4 12 507
Anopheles arabiensis Dongola AaraD1 AaraD1.7 13 862
Anopheles atroparvus EBRO AatrE2 AatrE2.1 14 080
Anopheles christyi ACHKN1017 AchrA1 AchrA1.6 11 150
Anopheles coluzzii Mali-NIH AcolM1 AcolM1.5 14 887
Anopheles culicifacies A A-37 AculA1 AculA1.5 14 714
Anopheles darlingi Coari AdarC3 AdarC3.6 10 963
Anopheles dirus WRAIR2 AdirW1 AdirW1.6 13 240
Anopheles epiroticus Epiroticus2 AepiE1 AepiE1.6 12 262
Anopheles farauti FAR1 AfarF2 AfarF2.4 13 325
Anopheles funestus FUMOZ AfunF1 AfunF1.7 13 920
Anopheles gambiae PEST AgamP4 AgamP4.8 13 769
Anopheles maculatus maculatus3 AmacM1 AmacM1.5 15 018
Anopheles melas CM1001059_A AmelC2 AmelC2.5 15 753
Anopheles merus MAF AmerM2 AmerM2.5 13 694
Anopheles minimus MINIMUS1 AminM1 AminM1.6 13 091
Anopheles quadriannulatus SANGWE AquaS1 AquaS1.7 13 950
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 PhumU2.3 11 711
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 ScalU1.2 16 874

Expression data

New experiments processed and added to the expression browser:

All Aedes aegypti RNA-seq experiments have been reprocessed using the new AaegL5 assembly and gene set. Microarray probes have also been remapped to the new gene set.

Population Biology/Insecticide Resistance

10 projects have been added:

  • Temporal distribution and insecticide resistance profile of two major arbovirus vectors Aedes aegypti and Aedes albopictus in Yaoundé, the capital city of Cameroon (VBP0000202: details, map, 8 collections, 100 samples, 99 phenotypes, 0 genotypes)
  • Mapping insecticide resistance and characterization of resistance mechanisms in Anopheles arabiensis (Diptera: Culicidae) in Ethiopia (VBP0000204: details, map, 26 collections, 480 samples, 448 phenotypes, 96 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, 4 collections, 162 samples, 0 phenotypes, 9410 genotypes)
  • Insecticide resistance status of three malaria vectors, Anopheles gambiae (s.l.), An. funestus and An. mascarensis, from the south, central and east coasts of Madagascar (VBP0000206: details, map, 232 collections, 232 samples, 217 phenotypes, 45 genotypes)
  • Current Susceptibility Status of Malaysian Culex quinquefasciatus (Diptera: Culicidae) Against DDT, Propoxur, Malathion, and Permethrin (VBP0000207: details, map, 28 collections, 28 samples, 112 phenotypes, 0 genotypes)
  • First molecular genotyping of voltage gated sodium channel alleles in Culex quinquefasciatus populations in Malaysia (VBP0000208: details, map, 14 collections, 14 samples, 0 phenotypes, 42 genotypes)
  • Cow-baited tents are highly effective in sampling diverse Anopheles malaria vectors in Cambodia (VBP0000209: details, map, 3 collections, 225 samples, 94 phenotypes, 0 genotypes)
  • Insecticide resistance status of malaria vectors in Lao PDR (VBP0000210: details, map, 133 collections, 250 samples, 285 phenotypes, 84 genotypes)
  • Insecticide resistance in Anopheles arabiensis from Ethiopia (2012–2016): a nationwide study for insecticide resistance monitoring (VBP0000211: details, map, 33 collections, 369 samples, 297 phenotypes, 213 genotypes)
  • Malaria vectors in the Democratic Republic of the Congo: the mechanisms that confer insecticide resistance in Anopheles gambiae and Anopheles funestus (VBP0000203: details, map, 2 collections, 31 samples, 28 phenotypes, 7 genotypes)
35 projects have been updated (most of these were to make the genotype data consistent for visualisaion in the new genotype map view):
  • Novel mutations on the ace-1 gene of the malaria vector Anopheles albimanus provide evidence for balancing selection in an area of high insecticide resistance in Peru (VBP0000185: details, map, 3 collections, 3 samples, 0 phenotypes, 12 genotypes)
  • Status of insecticide resistance in high‑risk malaria provinces in Afghanistan (VBP0000131: details, map, 77 collections, 77 samples, 40 phenotypes, 12 genotypes)
  • Characterizing the insecticide resistance of Anopheles gambiae in Mali (VBP0000132: details, map, 47 collections, 47 samples, 52 phenotypes, 90 genotypes)
  • Contrasting patterns of insecticide resistance and knockdown resistance (kdr) in the dengue vectors Aedes aegypti and Aedes albopictus from Malaysia (VBP0000135: details, map, 24 collections, 48 samples, 101 phenotypes, 96 genotypes)
  • Multiple-Insecticide Resistance and Classic Gene Mutations to Japanese Encephalitis Vector Culex tritaeniorhynchus from China (VBP0000145: details, map, 12 collections, 12 samples, 41 phenotypes, 24 genotypes)
  • Preliminary assessment of the potential role of urbanization in the distribution of carbamate and organophosphate resistant populations of Culex species in Ghana (VBP0000147: details, map, 14 collections, 14 samples, 36 phenotypes, 10 genotypes)
  • Insecticide susceptibility of natural populations of Anopheles coluzzii and Anopheles gambiae (sensu stricto) from Okyereko irrigation site, Ghana, West Africa (VBP0000149: details, map, 3 collections, 3 samples, 7 phenotypes, 8 genotypes)
  • Susceptibility of Anopheles gambiae to insecticides used for malaria vector control in Rwanda (VBP0000152: details, map, 38 collections, 38 samples, 140 phenotypes, 28 genotypes)
  • Patterns of insecticide resistance and knock down resistance (kdr) in malaria vectors An. arabiensis, An. coluzzii and An. gambiae from sympatric areas in Senegal (VBP0000156: details, map, 20 collections, 60 samples, 0 phenotypes, 114 genotypes)
  • Discovery of Point Mutations in the Voltage-Gated Sodium Channel from African Aedes aegypti Populations: Potential Phylogenetic Reasons for Gene Introgression (VBP0000160: details, map, 14 collections, 19 samples, 16 phenotypes, 40 genotypes)
  • Circumsporozoite protein rates, blood-feeding pattern and frequency of knockdown resistance mutations in Anopheles spp. in two ecological zones of Mauritania (VBP0000165: details, map, 17 collections, 17 samples, 12 phenotypes, 12 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 (VBP0000167: details, map, 20 collections, 20 samples, 0 phenotypes, 20 genotypes)
  • Evidence of multiple insecticide resistance mechanisms in Anopheles gambiae populations in Bangui, Central African Republic (VBP0000168: details, map, 7 collections, 14 samples, 42 phenotypes, 14 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 (VBP0000171: details, map, 9 collections, 9 samples, 27 phenotypes, 4 genotypes)
  • Insecticide susceptibility of Anopheles coluzzii and Anopheles gambiae mosquitoes in Ibadan, South-West Nigeria (VBP0000172: details, map, 14 collections, 14 samples, 13 phenotypes, 16 genotypes)
  • Presence of susceptible wild strains of Anopheles gambiae in a large industrial palm farm located in Aboisso, South-Eastern of Côte d’Ivoire (VBP0000183: details, map, 3 collections, 3 samples, 6 phenotypes, 8 genotypes)
  • Species Identification and Resistance Status of Anopheles gambiae s.l. (Diptera: Culicidae) Mosquitoes in Guinea (VBP0000188: details, map, 19 collections, 19 samples, 8 phenotypes, 24 genotypes)
  • Knockdown resistance (kdr) of the voltage-gated sodium channel gene of Aedes aegypti population in Denpasar, Bali, Indonesia (VBP0000189: details, map, 6 collections, 6 samples, 0 phenotypes, 12 genotypes)
  • Insecticide resistance is mediated by multiple mechanisms in recently introduced Aedes aegypti from Madeira Island (Portugal) (VBP0000195: details, map, 16 collections, 16 samples, 8 phenotypes, 32 genotypes)
  • Multiple mechanisms of resistance to pyrethroids in Anopheles gambiae s.l populations in Niger (VBP0000196: details, map, 7 collections, 63 samples, 52 phenotypes, 14 genotypes)
  • Dynamics of pyrethroid resistance in malaria vectors in southern Benin following a large scale implementation of vector control interventions (VBP0000150: details, map, 184 collections, 184 samples, 59 phenotypes, 224 genotypes)
  • Multi-country Survey Revealed Prevalent and Novel F1534S Mutation in Voltage-Gated Sodium Channel (VGSC) Gene in Aedes albopictus (VBP0000136: details, map, 12 collections, 12 samples, 2 phenotypes, 48 genotypes)
  • When intensity of deltamethrin resistance in Anopheles gambiae s.l. leads to loss of Long Lasting Insecticidal Nets bio-efficacy: a case study in north Cameroon (VBP0000141: details, map, 12 collections, 12 samples, 14 phenotypes, 9 genotypes)
  • Spatial and Temporal Trends in Insecticide Resistance among Malaria Vectors in Chad Highlight the Importance of Continual Monitoring (VBP0000142: details, map, 33 collections, 42 samples, 130 phenotypes, 18 genotypes)
  • Relationship between insecticide resistance and kdr mutations in the dengue vector Aedes aegypti in Southern China (VBP0000144: details, map, 5 collections, 5 samples, 10 phenotypes, 30 genotypes)
  • Multiple Insecticide Resistance in the Malaria Vector Anopheles funestus from Northern Cameroon Is Mediated by Metabolic Resistance Alongside Potential Target Site Insensitivity Mutations (VBP0000151: details, map, 3 collections, 10 samples, 28 phenotypes, 12 genotypes)
  • Exposure to deltamethrin affects development of Plasmodium falciparum inside wild pyrethroid resistant Anopheles gambiae s.s. mosquitoes in Uganda (VBP0000161: details, map, 1 collections, 4 samples, 2 phenotypes, 4 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 (VBP0000170: details, map, 1 collections, 526 samples, 0 phenotypes, 1052 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 (VBP0000173: details, map, 28 collections, 28 samples, 48 phenotypes, 96 genotypes)
  • Susceptibility profile and metabolic mechanisms involved in Aedes aegypti and Aedes albopictus resistant to DDT and deltamethrin in the Central African Republic (VBP0000178: details, map, 26 collections, 26 samples, 69 phenotypes, 8 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, 12 genotypes)
  • Combined target site (kdr) mutations play a primary role in highly pyrethroid resistant phenotypes of Aedes aegypti from Saudi Arabia (VBP0000181: details, map, 34 collections, 34 samples, 32 phenotypes, 24 genotypes)
  • Insecticide resistance patterns in Uganda and the effect of indoor residual spraying with bendiocarb on kdr L1014S frequencies in Anopheles gambiae s.s. (VBP0000184: details, map, 34 collections, 34 samples, 29 phenotypes, 36 genotypes)
  • Does insecticide resistance contribute to heterogeneities in malaria transmission in The Gambia? (VBP0000174: details, map, 16 collections, 44 samples, 45 phenotypes, 37 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) (VBP0000164: details, map, 19 collections, 21 samples, 40 phenotypes, 24 genotypes)

Variation Data

Summary of available variation data by organism

Reference speciesSNP calls (million)Indel calls (million)Last dataset updateLast variation effect update
Aedes aegypti 0.29 0.004 2017-12 2017-12
Anopheles arabiensis 10.2 0.98 2014-10 2017-12
Anopheles culicifacies 9.15 0.88 2014-10 2017-12
Anopheles epiroticus 3.28 0.25 2014-10 2017-12
Anopheles farauti 6.5 0.75 2015-062017-12
Anopheles funestus 12.9 0.47 2014-102017-12
Anopheles gambiae 7.2 1.5 2017-122017-12
Anopheles melas 3.7 0.41 2015-062017-12
Anopheles merus 6.1 0.53 2015-062017-12
Anopheles minimus 4.21 0.22 2014-10 2017-12
Anopheles quadriannulatus 10.1 0.89 2014-102017-12
Anopheles sinensis 5.84 0.41 2015-06 2017-12
Anopheles stephensi SDA-500 5.8 0.57 2014-10 2017-12
Anopheles stephensi Indian 0.37 2014-10 2017-12
Ixodes scapularis 1.78 2015-02 2017-12

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..

Future releases

The next VectorBase release (VB-2018-02) is scheduled for late February.

Known issues

  • Alignment based cross references are missing for some VectorBase species and will be regenerated in the February 2018 release.
  • The reprocessed Aedes aegypti differential expression data has been compared with the previous release and is qualitatively similar except for the experiment comparing domestic and forest strains, which appears to have very low amounts of differential expression and high p-values. We are diagnosing this and hope to have this resolved for the February release. The Aedes expression map will be updated when this remedial work is completed.

Please report any problems to the helpdesk.

Release date: 
Monday, December 11, 2017