Danio rerio
(NHGRI Press Photos)

The May 2005 zebrafish (Danio rerio) Zv5 assembly was produced by The Wellcome Trust Sanger Institute in collaboration with the Max Planck Institute for Developmental Biology in Tuebingen, Germany, and the Netherlands Institute for Developmental Biology (Hubrecht Laboratory), Utrecht, The Netherlands.

Sample position queries

A genome position can be specified by the accession number of an mRNA or EST, a scaffold range, or keywords from the GenBank description of an mRNA. The following list provides examples of various types of position queries for the zebrafish genome. Note that some position queries (e.g. "huntington") may return matches to the mRNA records of other species. In these cases, the mRNAs are mapped to their homologs in zebrafish. See the User Guide for more help.

   Genome Browser Response:

chr1   Displays all of chromosome 1
chr1:1-200000   Displays first two hundred thousand bases of chromosome 1
chr1:100000+2000 Displays a region of chr 1 that spans 2000 bases, starting with position 100000

U30710   Displays region containing zebrafish mRNA with GenBank accession number U30710
AA658622   Displays region containing zebrafish EST with GenBank accession AA658622

p53   Lists mRNAs related to the p53 tumor suppressor
pseudogene mRNA   Lists transcribed pseudogenes but not cDNAs, in GenBank
homeobox caudal   Lists mRNAs for caudal homeobox genes in GenBank
zinc finger   Lists many zinc finger mRNAs
kruppel zinc finger   Lists only kruppel-like zinc fingers
huntington   Lists mRNAs associated with Huntington's disease

porter   Lists mRNAs deposited by scientists named Porter
Amsterdam,A.   Lists mRNAs deposited by co-author A. Amsterdam

Use this last format for author queries. Although GenBank requires the search format Amsterdam A, internally it uses the format Amsterdam,A.

Assembly details

The Zv5 assembly consists of 1,630,306,866 bp in 16,214 scaffolds (N50 = 1,116,981 bp) with a sequence coverage of approximately 6.5-7x. The assembly has been tied to the FPC map (data freeze 15th February, 2005) and contains 699 Mb from 4,519 sequenced clones.

This assembly was constructed using two different strategies. In the first, a whole genome shotgun (WGS) approach was used. DNA from 1000 five-day-old Tuebingen embryos was used to generate plasmid and fosmid libraries. The libraries were sequenced and the resulting traces were assembled with the Sanger Institute assembler, Phusion. The second approach used traditional clone mapping and sequencing techniques to produce a higher quality genome sequence. BAC libraries were selected and fingerprinted to generate a fingerprint contig (FPC) map. From this map, a tiling path was calculated that covered the genome sequence clone-by-clone. Clones from this path were selected for high quality sequencing and then pieced together to form the genome sequence.

74% of the sequence (1,200,129,620 bp) is in FPC contigs and is tied to chromosomes 1-25. These contigs provided a template for placing the unfinished sequence. The remaining sequence was filled with WGS contigs using a combination of sequence alignment and BAC end positions as well as features such as zebrafish cDNAs and markers. 183,993,739 bp of sequence is in 265 scaffolds tied to unplaced FPC contigs and there are 246,183,507 bp in 14,676 NA scaffolds. The WGS assembly consists of 20,541,433 reads totaling 14,160,626,498 bp and this includes an additional set of 6,882,050 reads from a new library generated from a single Tuebingen double haploid zebrafish. Reads were clustered using Phusion, and Phrap was used to assemble clusters and for consensus generation. The resulting 247,928 contigs have an N50 size of 20,629 bp. From these, 105,987 scaffolds or supercontigs were created with an N50 size of 687,451 bp.

The Sanger Institute notes there is high level of misassembly present in this release due to the large amount of polymorphism in the DNA source. Regions where the physical map is incomplete or contains gaps have sequence with a higher number of misassemblies. Highly variable regions within the genome posed assembly difficulties, most likely because the sequences originated from different haplotypes. This also results in assembly dropouts and duplications. For more information about this assembly, see the Sanger Institute page for the Danio rerio Sequencing Project.

Downloads of the Zebrafish data and annotations can be obtained from the UCSC FTP site or Downloads page. This data set has specific conditions for use. The danRer1 annotation tracks were generated by UCSC and collaborators worldwide. Special thanks to the Zebrafish Genome Initiative at Children's Hospital in Boston, MA, USA for their collaboration on this release. See the Credits page for a detailed list of the organizations and individuals who contributed to the success of this release.