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/
In my opinion the Zv9 assembly is not as good as Zv7 or Zv8. Several of the gene families, a surprising amount, that we study in a wide variety of vertebrate genomes now have members on those contigs that haven't been mapped to chromosomal locations. Several others have shifted location from one chromosome to another. Previously we have studied these genome regions (up to 10 MB) in several zebrafish genome assemblies for conserved synteny with other vertebrate genomes, and the Zv9 assembly seems to be faulty in several instanced. I will continue working on Zv7.
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