PMID- 17597531 OWN - NLM STAT- MEDLINE DCOM- 20070904 LR - 20230503 IS - 1471-2164 (Electronic) IS - 1471-2164 (Linking) VI - 8 DP - 2007 Jun 27 TI - Definition of the zebrafish genome using flow cytometry and cytogenetic mapping. PG - 195 AB - 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. CONCLUSION: 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. FAU - Freeman, Jennifer L AU - Freeman JL AD - Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA. jfreeman7@partners.org FAU - Adeniyi, Adeola AU - Adeniyi A FAU - Banerjee, Ruby AU - Banerjee R FAU - Dallaire, Stephanie AU - Dallaire S FAU - Maguire, Sean F AU - Maguire SF FAU - Chi, Jianxiang AU - Chi J FAU - Ng, Bee Ling AU - Ng BL FAU - Zepeda, Cinthya AU - Zepeda C FAU - Scott, Carol E AU - Scott CE FAU - Humphray, Sean AU - Humphray S FAU - Rogers, Jane AU - Rogers J FAU - Zhou, Yi AU - Zhou Y FAU - Zon, Leonard I AU - Zon LI FAU - Carter, Nigel P AU - Carter NP FAU - Yang, Fengtang AU - Yang F FAU - Lee, Charles AU - Lee C LA - eng GR - WT_/Wellcome Trust/United Kingdom GR - R01 CA111560/CA/NCI NIH HHS/United States GR - R01-CA111560/CA/NCI NIH HHS/United States PT - Journal Article PT - Research Support, N.I.H., Extramural PT - Research Support, Non-U.S. Gov't DEP - 20070627 PL - England TA - BMC Genomics JT - BMC genomics JID - 100965258 SB - IM MH - Animals MH - Chromosome Mapping MH - Chromosomes, Artificial, Bacterial MH - Cytogenetics/*methods MH - Flow Cytometry/*methods MH - Genetic Techniques MH - *Genome MH - Genomic Library MH - Genomics MH - In Situ Hybridization, Fluorescence MH - Microscopy, Fluorescence MH - Models, Genetic MH - Telomere/ultrastructure MH - Zebrafish PMC - PMC1925092 EDAT- 2007/06/29 09:00 MHDA- 2007/09/05 09:00 PMCR- 2007/06/27 CRDT- 2007/06/29 09:00 PHST- 2007/02/07 00:00 [received] PHST- 2007/06/27 00:00 [accepted] PHST- 2007/06/29 09:00 [pubmed] PHST- 2007/09/05 09:00 [medline] PHST- 2007/06/29 09:00 [entrez] PHST- 2007/06/27 00:00 [pmc-release] AID - 1471-2164-8-195 [pii] AID - 10.1186/1471-2164-8-195 [doi] PST - epublish SO - BMC Genomics. 2007 Jun 27;8:195. doi: 10.1186/1471-2164-8-195.