Custom gene editing rewrites zebrafish DNA

Researchers led by Stephen Ekker, a molecular biologist at the Mayo Clinic in Rochester, Minnesota, have for the first time made custom changes to parts of the zebrafish (Danio rerio) genome, using artificial enzymes to cut portions of DNA out of targeted positions in a gene sequence, and replace them with synthetic DNA. The work is published in Nature. Ekker and his colleagues are the first to use artificial TALENs for genome editing in live zebra fish larvae. TALENs have the potential to work on any DNA sequence and cause permanent modifications. They also allow faster analysis of induced mutations — in some cases, the team found, it is possible to observe effects in the injected larvae immediately.

Read more: Nature-doi:10.1038/nature.2012.11463

Zv9, the most recent genome assembly for zebrafish.

The zebrafish (Danio rerio) is an important model organism for the study of vertebrate development and disease, organ function, behavior, and toxicology. Some of the features that make the zebrafish so experimentally amenable include its short generation time, large numbers of embryos produced per mating, and the development of transparent embryos outside the mother, allowing all stages of development to be observed. The Sanger Institute started the zebrafish genome sequencing project in 2001 and has released several genome assemblies, the latest is Zv9 .

Ninth assembly, Zv9 of the zebrafish genome released is recently been made available in the UCSC Genome Browser. This assembly comprises a total sequence length of 1.4 Gb in 4,560 scaffolds. The remaining gaps were filled with sequence from WGS31, a combined Illumina and capillary assembly. The assembly integration process involves sequence alignments as well as cDNA, marker and BAC/Fosmid end sequence placements. The sequences that are based on clone contigs or are linked to chromosomes via markers are named 'Zv9_scaffold' followed by a number. The WGS contigs that could not be placed onto chromosomes are named 'Zv9_NA' followed by a number.

This preliminary assembly was produced by The Wellcome Trust Sanger Institute, UK.

http://www.sanger.ac.uk/Projects/D_rerio/