Zebrafish Genome Sequence handed over to Genome Reference Consortium
After the release of the integrated genome assembly Zv9 by the Wellcome Trust Sanger Institute in July 2010, the zebrafish genome sequencing project has now reached maintenance stage and has been handed over to the Genome Reference Consortium (GRC,http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/index.shtml), comprising the Sanger Institute (mapping/sequencing and informatics), the NCBI (informatics), the EBI (informatics for variation data) and the Genome Center at WashU (mapping/sequencing).
The GRC was formed to further improve and correct high quality finished genome assemblies such as human and mouse by assessing mapping information, re-sequencing problematic regions and identifying and sequencing clones covering missing regions. Another main focus for the improvement of genome assemblies is assessing variation data and adding alternative variants to correctly represent genome diversity and provide more robust substrates for genome analysis.
The GRC has recognised the high quality of the current zebrafish genome sequence and its importance as a model organism genome. The consortium has therefore made an ongoing commitment to further improve the zebrafish genome sequence and to maintain it for an unlimited time in the future. The GRC's web pages are available to the community to report genome issues and track progress of the clone path development and assembly generation.
For the zebrafish research community's daily undertakings, nothing much changes. The Sanger Institute as part of the GRC is still driving the ongoing refinements of the genome sequence and its manual and automated annotation. We are still providing support on-line, in workshops and at meetings. All present resources will be kept up to date and the collaboration with ZFIN to annotate all zebrafish genes is ongoing. The community members can report genome issues either to the GRC directly or -- as before -- to zfish-help@sanger.ac.uk.
Please send us your questions and comments to zfish-help@sanger.ac.uk or to the GRC directly (see below). Your input is highly valued and helps us to improve the support for your research!
Best wishes,
Kerstin Howe on behalf of the GRC
Links:
GRC home page: http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/index.shtml
GRC zebrafish project page: http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/zebrafish/index.shtml
GRC 'report a genome issue': http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc_new/ReportAnIssue.shtml
GRC contact: http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc_new/contact.shtml
Zebrafish Genome Project home page: http://www.sanger.ac.uk/Projects/D_rerio/
Ensembl: http://www.ensembl.org/Danio_rerio/Info/Index (http://pre.ensembl.org/Danio_rerio/Info/Index)
Vega: http://vega.sanger.ac.uk/Danio_rerio/Info/Index