Release VB-2013-12

Overview

We are pleased to announce the December release of VectorBase (VB-2013-12):

  • First-pass annotations for the remaining seven Anophelines are complete and available for browsing, download and similarity searches
  • Assembly and annotation updates for Aedes aegypti AaegL2.1 and Anopheles darlingi AdarC2.1
  • VectorBase contains nearly 100 RNAseq experiments from nine species. See the new interface to explore. Coverage plots in the genome browser are now presented as bigwig files rather than bam, which gives a significant page load time improvement.
  • Two new tutorials have been added and twelve tutorials have been updated.
  • There are now 11 VectorBase practice exercises! These are the compilation of all hands-on exercises from this year's workshops. When appropriate, sample files are included. Follow this link to get started with BioMart.
  • Many FAQs have been updated, most notably the 18 for Community Annotation Portal (CAP) and 33 for the Genome Browser. Follow this link to try the FAQ: Region in detail.
  • Two microarray experiments and one population biology project are now available.

Genomes

VectorBase is committed to a new release every two months with all data freely available for public use based on NIH/NIAID policy. A list of these changes and the state of current versions on this date (e.g., current gene sets) can be found on the Releases section of VectorBase.

For your species of interest, click on Organism, Strain, Assembly, or Gene set to find the Genome Browser link (which looks like this:  ).

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

Genome annotation

Release of the first-pass annotations for 7 Anopheline genomes
The Anopheles Genomes Cluster announce the final set of genome annotations for the remaining seven Anopheline genomes. These initial annotations are also available for searching via BLAST and download.

Release of the Anopheles darlingi genome assembly and annotations
The An. darlingiCoari strain has an improved genome assembly and a complete re-annotation based on the recent publication The genome of An. darlingi, the main neotropical malaria vector (Marinotti et al 2013). A total of 10,481 predicted protein-coding genes were annotated, 72% of which have their closest counterpart in Anopheles gambiae and 21% have highest similarity with other mosquito species.

Release of the Aedes aegypti genome assembly and annotations
A new geneset for Aedes aegypti AaegL2.1 is a significant update to the annotations incorporating models derived from RNAseq datasets as well as from the community. Many loci have been merged and 4,600 new UTRs have been added adding over 3.2 Mb of sequence to transcriptome. It is hoped that these changes will increase the volume of RNAseq data aligning to the transcriptome and improve sequence-based measures of gene expression.

Expression Data

Two experiments/publications regarding insecticide resistance in Anopheles gambiae have been added:

As usual, all expression resources have been updated to incorporate gene set changes (for this release, AaegL2.1 is fully supported).

Population Biology/Insecticide Resistance

A second large study from IRBase has been imported into the Population Biology resource/browser. It provides percent mortality data for a variety of insecticides in two anopheline species between 1991-2003 in various regions of Sri Lanka.

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 Aedine mitochondrial genes 2013-11
Anopheles Anopheles gambiae Anopheline mitochondrial genes 2013-11
Culex Culex quinquefasciatus Culicine mitochondrial genes 2013-11
Ixodidae and Argasidae Ixodes scapularis Ixodida mitochondrial genes 2013-11

Ontologies

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

Ontology Version Description
GAZ 1.512 A controlled vocabulary of geographic locations.
GO 2013-11-18 The gene ontology.
IDODEN 0.12 Beta release of an an ontology that describes all aspects of Dengue. Clinical data, epidemiological data, biological data concerning vertebrate hosts, vectors and viruses as well as interventions and attempts to control the disease.
IDOMAL 1.35 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. This version includes a section describing natural therapies and remedies.
MIRO 2.1 An ontology to describe mosquito populations, methods and mechanisms that are used to identify/monitor insecticide resistance.
TADS 1.22 An ontology to describe the anatomy of ticks.
TGMA 1.12 An ontology to describe the anatomy of mosquitoes. This version contains all the images from the book "Anatomical drawings of the biting flies".

Known issues

  • The newly added insecticide resistance project VBP0000014 has some minor curation/display issues which will be resolved in the February release.
  • VectorBase genes have the wrong version number in BioMart (0.5 instead of 1.0). This is being reloaded and should reflect the correct version later today

Please report any problems to the helpdesk.

Release date: 
Tuesday, December 10, 2013