Release VB_2012-10

Note, this is legacy information that refers to an older version of the VectorBase website.
Hyperlinks have been removed and URLs may no longer be valid.

Overview

We are pleased to announce the October release of VectorBase (VB-2012-10). Highlights of the October release of VectorBase (VB-2012-10) include:

  • Presites for the genomes of the sandflies: Phlebotomus papatasi and Lutzomyia longipalpis
  • New gene set for Anopheles gambiae (AgamP3.7)
  • Updated variation databases for Anopheles gambiae

Additionally, we have just completed a preview of the newly-designed, next generation VectorBase website. We invite you to try it out and provide constructive feedback on it. Nearly all of the content in the VB-2012-10 release is present in the preview site and available through a redesigned tab-driven navigation system. Details regarding this preview can be found below.

Genomes

VectorBase is please to release two pre-sites for Phlebotomus papatasi and Lutzomyia longipalpis. Both of these have been released in GenBank and details can be found below.

Fully released genomes, with gene predictions

Species Assembly Gene set GenBank WGS
Aedes aegypti Liverpool AaegL1 AaegL1.3 AAGE02000000
Anopheles gambiae PEST AgamP3 AgamP3.7 AAAB01000000
Culex quinquefasciatus JHB CpipJ1 CpipJ1.3 AAWU01000000
Ixodes scapularis Wikel IscaW1 IscaW1.2 ABJB01000000
Pediculus humanus USDA PhumU1 PhumU1.2 AAZO01000000

Pre-released genomes, with mapped data but no gene predictions

Species Assembly GenBank WGS Data available
Anopheles gambiae M AgamM1 ABKP00000000 Repeats, ESTs
Anopheles gambiae S AgamS1 ABKQ00000000 Repeats, ESTs
Lutzomyia longipalpis Jacobina LlonJ1 AJWK00000000 Repeats, SNAP
Phlebotomus papatasi Israel PpapI1 AJVK00000000 Repeats, SNAP
Rhodnius prolixus CDC RproC1 ACPB00000000 Repeats, ESTs, RNA-seq and protein similarities - GenScan ab initio predictions and EST-build genes.
Glossina morsitans Yale GmorY1 - Repeats, RNA-seq (via BAM files) - EST-build genes, SNAP ab initio predictions, MAKER gene predictions.
Anopheles darlingi AdarC1 ADMH00000000 Repeats, ENA and UniProtKB annotation.
Anopheles stephensi Indian Wild Type AsteI1 - Repeats, EST-build genes, SNAP ab initio predictions, MAKER gene predictions.

An. gambiae gene set AgamP3.7

The An. gambiae gene set has had a major update bringing in novel predictions and model corrections from both VectorBase staff (University of New Mexico/Harvard University) and community submissions. Over 1200 predictions have been updated as well as150 new loci, 87 merge events (>=2 canonical models now modeled by a single prediction) and 59 split events (single canonical model now modeled by >=2 predictions),

Variation Data

Variation data for two studies describing mapping of insecticide resistance in Africa have been included in this release. The studies are described in

  • Weetman, David, Wilding, Craig, Steen, Keith, Pinto, J. and Donnelly, Martin (2011) 'Gene Flow-Dependent Genomic Divergence Between Anopheles gambiae M and S Forms'. Molecular Biology and Evolution, Vol 29, Issue 1, pp. 279-291. (doi: 10.1093/molbev/msr199)
  • Weetman, David, Wilding, Craig, Steen, Keith, Morgan, John, Simard, Frederic and Donnelly, Martin (2010) 'Association Mapping of Insecticide Resistance in Wild Anopheles gambiae Populations: Major Variants Identified in a Low-Linkage Disequilbrium Genome'. PLoS ONE, Vol 5, Issue 10, e13140. (doi:10.1371/journal.pone.0013140)

These samples were typed using a Goldengate microarray platform, on a variety of samples from different geographical locations in Africa.

Population Location Collection_year Total_samples
Yaounde Cameroon 2006 735
Tororo Uganda 2008 214
Dodowa Ghana 2006 802
Antula Guinea-Bissau 1993 80

For some loci a large number of individuals may be noted next to the "resequencing" tag in the genetic variation data display section. This tag normally allows users to access sequence coverage data for the regions for all of the strains indicated, but as these samples were genotyped on a microarray chip this coverage data is not available. We are investigating ways to make the normal resequencing display functionality available.

Expression Data

A new dataset for An. gambiae has been added:

  • Desiccation stress, Wang et al. 2011

Mitochondrial gene summaries for VectorBase genera

Links to Mitochondrial data for the 4 main genera are presented below for convenience.

Genus/genera Reference species Mitochondrial gene resource Last updated
Aedes Aedes aegypti http://aaegypti.vectorbase.org/SequenceData/Mitochondria/ 2012-06-03
Anopheles Anopheles gambiae http://agambiae.vectorbase.org/SequenceData/Mitochondria/ 2012-06-03
Culex Culex quinquefasciatus http://cquinquefasciatus.vectorbase.org/SequenceData/Mitochondria/ 2012-06-03
Ixodidae and Argasidae Ixodes scapularis http://iscapularis.vectorbase.org/SequenceData/Mitochondria/ 2012-06-03

Ontologies

VectorBase supports four ontologies developed by IMBB with members of the research community. These are available for browsing and download.

Ontology Version Description
MIRO 2.0 An ontology to describe mosquito populations, methods and mechanisms that are used to identify/monitor insecticide resistance.
TGMA 1.10 An ontology to describe the anatomy of mosquitoes.
TADS 1.21 An ontology to describe the anatomy of ticks.
IDOMAL 1.2.4 An ontology to describe all aspects of malaria. Clinical data, epidemiological data, biological data concerning vertebrate hosts, vectors and parasites as well as interventions and attempts to control the disease.

Ontology browser

The Controlled Vocabulary/Ontology browser has been upgraded. Most noteworthy changes:

  • it is now possible to search for terms using synonyms
  • term synonyms are now listed along with the rest of the term's details
  • OBO flat files can be downloaded by using the links on the main page of the CV browser

Preview of newly designed website

The beta version of the website can be accessed at https://preview.vectorbase.org.The preview site is now the live site! This documentation is kept for historical record only. To help you get acclimated, here are five specific changes for review (among many):

  • We have redesigned the homepage to highlight data, tools and resources, FAQs and community interactions. We also anticipate user-focused customization (e.g., accessing previous analyses) in later versions of this site.
  • The BLAST tool has been improved based on prior feedback It is available at: https://preview.vectorbase.org/blast and under the “Tools” tab.
  • The search box in the upper right corner of all VectorBase pages can access a new unified search framework. All queries are filterable.
  • We have extended the organisms page (https://preview.vectorbase.org/organisms) and species pages (e.g. https://preview.vectorbase.org/organisms/anopheles-gambiae). This has allowed us to group current and emerging genomes in a scalable manner while also highlighting and archiving strain, assembly and gene build history.
  • The old help pages/wiki have been reallocated into new content under “Help” and “Community” tabs to consolidate these important documents into a single site and to facilitate search access (see #2 above).

We are interested in feedback about these changes using the Contact Us page or mail the the helpdesk.

Known issues

Biomart has not yet been updated with the new genomes; we anticpate this being released within a week.

Please report any problems to the helpdesk.

Release date: 
Tuesday, October 30, 2012