ZFIN and the Genome Reference Consortium

ZFIN is a member of the The Genome Reference Consortium (GRC), an international collaboration consisting of NCBI, the Wellcome Trust Sanger Institute, the McDonnell Genome Institute at Washington University, the European Bioinformatics Institute (EBI) and ZFIN. This consortium is tasked with ensuring that the reference assemblies for human, mouse, zebrafish and chicken are updated and improved through new data and analysis from genome centers and the research community.

The zebrafish specific GRC webpage (see Fig. 1) provides an overview of the zebrafish genome including an ideogram of the latest zebrafish assembly (GRCz11) and alternate loci scaffolds, downloadable build and tiling path files as well as links to genome assembly data and genome regions under review.  Zebrafish genome issues (see Fig. 2) can be browsed at the chromosome level, filtered by problem type or status or searched by gene, location, clone name or accession.

If you come across what you suspect is a problem in the build, search the list of genome issues and if it has yet to be reported, select the "Report and Issue" tab in the header (see Fig. 3) to report information about the potential problem in the build.  Be as complete as possible and provide location, flanking sequences and a description of the issue.  Genome annotators will evaluate the region, determine if an update to the genome is needed and submit data to create a new tiling path to improve the build with an update or "patch".

Figure 1

Figure 2

Figure 3