title: Definition of the zebrafish genome using flow cytometry and cytogenetic mapping.
abstract: BACKGROUND
  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.
  
  
  RESULTS
  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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA. jfreeman7@partners.org <jfreeman7@partners.org>
authors.forename: Jennifer L
authors.initials: JL
authors.lastname: Freeman
authors.forename: Adeola
authors.initials: A
authors.lastname: Adeniyi
authors.forename: Ruby
authors.initials: R
authors.lastname: Banerjee
authors.forename: Stephanie
authors.initials: S
authors.lastname: Dallaire
authors.forename: Sean F
authors.initials: SF
authors.lastname: Maguire
authors.forename: Jianxiang
authors.initials: J
authors.lastname: Chi
authors.forename: Bee Ling
authors.initials: BL
authors.lastname: Ng
authors.forename: Cinthya
authors.initials: C
authors.lastname: Zepeda
authors.forename: Carol E
authors.initials: CE
authors.lastname: Scott
authors.forename: Sean
authors.initials: S
authors.lastname: Humphray
authors.forename: Jane
authors.initials: J
authors.lastname: Rogers
authors.forename: Yi
authors.initials: Y
authors.lastname: Zhou
authors.forename: Leonard I
authors.initials: LI
authors.lastname: Zon
authors.forename: Nigel P
authors.initials: NP
authors.lastname: Carter
authors.forename: Fengtang
authors.initials: F
authors.lastname: Yang
authors.forename: Charles
authors.initials: C
authors.lastname: Lee
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D022202:Chromosomes, Artificial, Bacterial; D003582:Cytogenetics / Q000379:methods*; D005434:Flow Cytometry / Q000379:methods*; D005821:Genetic Techniques; D016678:Genome; D015698:Genomic Library; D023281:Genomics; D017404:In Situ Hybridization, Fluorescence; D008856:Microscopy, Fluorescence; D008957:Models, Genetic; D016615:Telomere / Q000648:ultrastructure; D015027:Zebrafish