Open Access Research article

Definition of the zebrafish genome using flow cytometry and cytogenetic mapping

Jennifer L Freeman12, Adeola Adeniyi1, Ruby Banerjee3, Stephanie Dallaire1, Sean F Maguire3, Jianxiang Chi3, Bee Ling Ng3, Cinthya Zepeda4, Carol E Scott3, Sean Humphray3, Jane Rogers3, Yi Zhou5, Leonard I Zon5, Nigel P Carter3, Fengtang Yang3 and Charles Lee12*

Author Affiliations

1 Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA

2 Harvard Medical School, Boston, Massachusetts 02115, USA

3 Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK

4 Centro de Ciencias Genomicas, Universidad Nacional Autónoma de México, Ap. Postal 565-A, Cuernavaca, Morelos, Mexico

5 Howard Hughes Medical Institute and Division of Hematology/Oncology, Children's Hospital and Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts 02115, USA

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BMC Genomics 2007, 8:195  doi:10.1186/1471-2164-8-195

Published: 27 June 2007



The zebrafish (Danio rerio) is an important vertebrate model organism system for biomedical research. The syntenic conservation between the zebrafish and human genome allows one to investigate the function of human genes using the zebrafish model. To facilitate analysis of the zebrafish genome, genetic maps have been constructed and sequence annotation of a reference zebrafish genome is ongoing. However, the duplicative nature of teleost genomes, including the zebrafish, complicates accurate assembly and annotation of a representative genome sequence. Cytogenetic approaches provide "anchors" that can be integrated with accumulating genomic data.


Here, we cytogenetically define the zebrafish genome by first estimating the size of each linkage group (LG) chromosome using flow cytometry, followed by the cytogenetic mapping of 575 bacterial artificial chromosome (BAC) clones onto metaphase chromosomes. Of the 575 BAC clones, 544 clones localized to apparently unique chromosomal locations. 93.8% of these clones were assigned to a specific LG chromosome location using fluorescence in situ hybridization (FISH) and compared to the LG chromosome assignment reported in the zebrafish genome databases. Thirty-one BAC clones localized to multiple chromosomal locations in several different hybridization patterns. From these data, a refined second generation probe panel for each LG chromosome was also constructed.


The chromosomal mapping of the 575 large-insert DNA clones allows for these clones to be integrated into existing zebrafish mapping data. An accurately annotated zebrafish reference genome serves as a valuable resource for investigating the molecular basis of human diseases using zebrafish mutant models.