Danio rerio
(NHGRI Press Photos)

The March 2006 zebrafish (Danio rerio) Zv6 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 Zv6 assembly consists of 1,626,077,335 bp in 6,653 scaffolds (N50 = 1,247,221 bp) with a sequence coverage of approximately 6.5-7x. The assembly, which has been tied to the FPC map with data freeze 12 March 2006, contains 1.02 Gb from 7,615 sequenced clones, 5,994 finished and 1,621 unfinished. Gaps are filled by sequence from the whole genome shotgun (WGS) assembly.

This assembly was constructed using two different strategies. In the first, a 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.

Clone sequences and WGS contigs were then integrated by considering sequence alignments, BAC end placements and zebrafish cDNAs and markers. Improvements to the integration algorithm allowed the placement of the WGS contigs that contained markers, but could not be linked to the FPC contigs. In cases where markers from different chromosomes appear on the same contig, priority has been given to the Heat Shock Diploid Cross Panel (HS) and the Boston MGH Cross Map (MGH). Some of these discrepancies may be attributed to misassemblies, but there may also be inconsistencies between the zebrafish marker panels.

95% of the sequence -- 1,547,299,723 bp including estimated gap sizes -- lies in scaffolds that are placed on chromosomes 1-25 (linkage groups 1-25) after integration of the WGS assembly with the clone sequences. Integration was achieved by consideration of a combination of sequence alignment and BAC end positions, as well as features such as zebrafish cDNAs and markers. 15,986,232 bp of the sequence are in 68 scaffolds tied to unplaced FPC contigs; 63,164,280 bp are in 2,898 NA scaffolds. The WGS assembly consists of 20,541,433 reads totaling 14,160,626,498 bp, including an additional set of 6,882,050 reads from a new library generated from a single Tuebingen doubled 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 (supercontigs) were created with an N50 size of 687,451 bp.

The Sanger Institute notes this assembly release is still preliminary. 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 false duplications. In addition, the regions covered by WGS contigs are lower quality sequence. For more information about this Zv6 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 danRer4 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 this release.