Release VB-2018-06
We are pleased to announce the June 2018 release of VectorBase (VB-2018-06):
- Updates to the gene sets for 4 species based on community annotation ( Anopheles merus, A. minimus, A. quadriannulatus, and Glossina morsitans).
- An assembly and minor gene set update for Anopheles atroparvus based on the publication "Partial-arm translocations in evolution of malaria mosquitoes revealed by high-coverage physical mapping of the Anopheles atroparvus genome." by Artemov et al.
- New Aedes aegypti variation data from the publication "Origin of a High-Latitude Population of Aedes aegypti in Washington, DC" by Gloria-Soria et al.
- The patch build quality control code used to analyse Apollo gene edist is now available on the VectorBase code site.
- Retirement of support for the Aedes aegypti AaegL3 assembly.
- In the December 2017 VectorBase release VectorBase announced the adoption of the new Aedes aegypti AaegL5 genome assembly produced by the Aedes aegypti Genome Working group. We have received a number of communications from the community that indicate people are encountering significant problems when working with the new gene set based on this assembly. The NCBI Aedes aegypti annotation release 101 (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Aedes_aegypti/101/) was a new de novo annotation using the Gnomon software (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/gnomon/), and as such differs significantly from the existing AaegL3 gene set. VectorBase has worked with the NCBI to attempt to map existing stable gene ids between the assemblies, but given the nature of the different assembly and predicted gene models this has not always been possible. Improved contiguation of the AaegL5 assembly has resulted in significant gene model changes at a number of loci as a result of split/merge events to the AaegL3 gene models. Gene models may also have changed based on the available RNAseq data used in the new AaegL5 annotation. The VectorBase community is the final arbiters of the gene models for all the organisms that we support, and we provide the Apollo gene editor software to allow our users to correct gene models based on their own data or expertise. We strongly encourage the community to use this mechanism to improve the AaegL5 gene set, and we provide training and support to aid in this effort (https://www.vectorbase.org/apollo).
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VectorBase will continue to provide access to the AaegL3 genome browser (https://www.vectorbase.org/organisms/aedes-aegypti) until the December 2018 release (currently scheduled for the week of 19th December, 2018). We are unable to support alternate gene sets from different assemblies for the same organism via the BioMart software and the VectorBase search facility. If you still require access to BioMart based on AaegL3 you can use the Ensembl Genomes site ( http://metazoa.ensembl.org/biomart/martview ) which continues to host the old VectorBase AaegL3 browser and BioMart instance. VectorBase also provides a number of other resources to help with the transition between assemblies and older gene sets.
https://www.vectorbase.org/downloads?field_organism_taxonomy_tid%5B%5D=3...
- Aedes-aegypti-Liverpool_MAPPINGS_AaegL3.5-AaegL5.1.txt - Stable gene ID mapping between genesets AaegL3.5 and AaegL5.1
- Aedes-aegypti-Liverpool_MAPPINGS_AaegL3.3-AaegL3.4.txt - Stable gene ID mapping between genesets AaegL3.3 and AaegL3.4 (RNA gene update)
- Aedes-aegypti-Liverpool_MODIFICATIONS_AaegL2.2-AaegL3.1-ncRNA.txt - Liverpool strain gene prediction stable identifier mapping for ncRNA from the AaegL2.2 to AaegL3.1 geneset
- If additional files mapping identifiers from alternative sources such as UniProt are required please contact us.
- VectorBase currently plans to discontinue support for the AaegL3 assembly after the December 2018 release. We wish to help the community as much as possible with the migration to the AaegL5 assembly and associated gene set, but we need as much information from you as possible to help us plan this process. If the loss of AaegL3 support after December 2018 will cause problems for your work please contact us before August 30th 2018 with as detailed a description of what support you will need as possible.
- Added a method to view blast hits in Apollo for annotation. See here for more information
- New FAQ (click here) describing some of the aspects of Apollo automatic emails.
- Gene Knowledge Cards have been added to site search to provide an easy access of useful information. Try it out!
- Added the option for a boolean "NOT" in the Population Biology Map to allow for an exclusion filter
- Added Population Biology Map help tooltips on hover over.
- Additional Improvements and bugfixes have been made to the Population Biology Map and underlying data.
Genomes
Released genomes, with gene predictions
Expression data
New experiments processed and added to the expression browser:
- Dehydration of adult females (Hagan et al., 2018) Culex pipiens RNA-seq experiment
- Permethrin resistant Cyp-1 strain (Main et al., 2018) Anopheles coluzzii RNA-seq experiment
Population Biology/Insecticide Resistance
26 projects have been added:
- Monitoring resistance to insecticides in Aedes aegypti populations from Brazil (VBP0000268: details, map, 369 collections, 678 samples, 4290 phenotypes, 0 genotypes)
- The current insecticide resistance status of Anopheles gambiae (s.l.) (Culicidae) in rural and urban areas of Bouaké, Côte d’Ivoire (VBP0000270: details, map, 5 collections, 19 samples, 40 phenotypes, 56 genotypes)
- Larval density mediates knockdown resistance to pyrethroid insecticides in adult Aedes aegypti (VBP0000271: details, map, 1 collections, 945 samples, 100 phenotypes, 3356 genotypes)
- Frequency and intensity of pyrethroid resistance through the CDC bottle bioassay and their association with the frequency of kdr mutations in Aedes aegypti (Diptera: Culicidae) from Mexico. (VBP0000272: details, map, 11 collections, 52 samples, 123 phenotypes, 44 genotypes)
- Fine-scale spatial and temporal heterogeneities in insecticide resistance profiles of the malaria vector, Anopheles arabiensis in rural south-eastern Tanzania (VBP0000273: details, map, 6 collections, 12 samples, 432 phenotypes, 0 genotypes)
- Insecticide resistance in Anopheles arabiensis populations from Dakar and its suburbs: role of target site and metabolic resistance mechanisms (VBP0000274: details, map, 14 collections, 15 samples, 2256 phenotypes, 0 genotypes)
- Evaluation of Insecticides Susceptibility and Malaria Vector Potential of Anopheles annularis s.l. and Anopheles vagus in Assam, India (VBP0000275: details, map, 2 collections, 20 samples, 20 phenotypes, 0 genotypes)
- Insecticide resistance status of the malaria mosquitoes: Anopheles gambiae and Anopheles funestus in eastern and northern Uganda (VBP0000276: details, map, 4 collections, 12 samples, 24 phenotypes, 16 genotypes)
- Resting and feeding preferences of Anopheles stephensi in an urban setting, perennial for malaria (VBP0000277: details, map, 2 collections, 9 samples, 14 phenotypes, 0 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)
17 projects have been updated (usually to fix minor data inconsistencies):
- Malaria Atlas Project: Global distribution of observed malaria vector species (Europe) (VBP0000026: details, map, 1910 collections, 3026 samples, 0 phenotypes, 0 genotypes)
- Malaria Atlas Project: Global distribution of observed malaria vector species (Americas) (VBP0000027: details, map, 2998 collections, 4129 samples, 0 phenotypes, 0 genotypes)
- Malaria Atlas Project: Global distribution of observed malaria vector species (Africa) (VBP0000028: details, map, 6137 collections, 9582 samples, 0 phenotypes, 0 genotypes)
- Malaria Atlas Project: Global distribution of observed malaria vector species (Asia) (VBP0000029: details, map, 7972 collections, 13587 samples, 0 phenotypes, 0 genotypes)
- Sandfly surveillance in Cyrpus, 2011-2013 (VBP0000229: details, map, 135 collections, 3757 samples, 0 phenotypes, 0 genotypes)
- Origin of a High-Latitude Population of Aedes aegypti in Washington, DC (VBP0000201: details, map, 7 collections, 292 samples, 0 phenotypes, 6952 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)
- Composition of Anopheles mosquitoes, their blood-meal hosts, and Plasmodium falciparum infection rates in three islands with disparate bed net coverage in Lake Victoria, Kenya (VBP0000221: details, map, 11 collections, 11 samples, 132 phenotypes, 0 genotypes)
- First data on resistance to pyrethroids in wild populations of Aedes albopictus from Spain (VBP0000239: details, map, 4 collections, 4 samples, 24 phenotypes, 0 genotypes)
- Host attraction and biting behaviour of Anopheles mosquitoes in South Halmahera, Indonesia (VBP0000241: details, map, 1235 collections, 1235 samples, 6175 phenotypes, 0 genotypes)
- Mosquito surveillance in Manatee County, Florida, USA. 2013 (VBP0000253: details, map, 2516 collections, 15620 samples, 0 phenotypes, 0 genotypes)
- Susceptibility of Aedes albopictus from China to insecticides, and mechanism of DDT resistance (VBP0000024: details, map, 15 collections, 15 samples, 114 phenotypes, 0 genotypes)
- Potential for organophosphate resistance in Aedes aegypti (Diptera, Culicidae) in the Caribbean area and neighbouring countries (VBP0000097: details, map, 31 collections, 31 samples, 105 phenotypes, 0 genotypes)
- President's Malaria Initiative (PMI) insecticide susceptibility data (VBP0000123: details, map, 4688 collections, 4688 samples, 4618 phenotypes, 31 genotypes)
- Composition and genetics of malaria vector populations in the Central African Republic (VBP0000155: details, map, 15 collections, 37 samples, 109 phenotypes, 0 genotypes)
- ANVR 1st dataset (VBP0000009: details, map, 228 collections, 228 samples, 456 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)
Improvements have been made to the PopBio Map interface - including the return of a conventional "date picker" in the date-based filtering and a new "NOT" Boolean search feature (hold down the ctrl or command key while clicking on an autocomplete suggestion).
Variation Data
Summary of available variation data by organism
| Reference species | Assembly | SNP calls | Indel calls |
|---|---|---|---|
| Aedes aegypti Liverpool | AaegL3 | 332,445 | 4,081 |
| Aedes aegypti LVP_AGWG | AaegL5 | 313,612 | 1,761 |
| 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 | 59,236,057 | 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 Channel to watch all our video tutorials. The video slides (including demo outlines), are in our regular tutorial pages.
Future releases
The next VectorBase release (VB-2018-08) is scheduled for late August.
Other known issues
- Some samples with SNP-chip variation data that is available in the genome browser have not yet been added to PopBio project VBP0000201. This will be resolved for the next release.
Please report any problems to the helpdesk.
Release date:
Thursday, June 28, 2018
