Beyond the Identification of Transcribed Sequences: Functional and Expression Analysis

9th Annual Workshop, October 28-31, 1999

Co-sponsored by the U.S. Department of Energy


Construction of a whole genome transcribed sequence map for the zebrafish Danio Rerio

W. Brad Barbazuk1, Ian Korf1, Frank Li2, John McPherson1 and Steve Johnson2

1Genome Sequencing Center, Washington University School of Medicine, St. Louis, Missouri, USA
2Dept of Genetics, Washington University School of Medicine, St. Louis, Missouri, USA

The zebrafish is an important vertebrate model for mutational analysis of developmental processes.  Development of zebrafish genomic resources serves to expedite gene identification, high resolution physical map construction and the molecular localization and identification of mutated genes.  The construction of a whole genome radiation hybrid map provides an invaluable resource for both the initiation of positional cloning projects and the production of physical maps to support genomic sequencing.  We are developing a radiation hybrid map of the zebrafish genome map using the LN54 whole genome radiation hybrid panel constructed by Marc Ekker.  In collaboration with Niel Hukreide, over 1000  markers derived from genetically mapped CA repeat sequences, zebrafish EST sequences and mapped genes have been typed across the LN54 panel to produce our framework map.  We are now attempting to increase the marker density of this map by typing an additional 5000 STSs, and are providing a further 5000 STSs to RH mapping efforts undertaken by other members of the zebrafish community.  

This effort is synchronized with the zebrafish EST project being conducted at Genome Sequencing Center in St. Louis.  ESTs generated by this project serve as substrates from which STS markers are being developed.  We have currently placed over 500 zebrafish ESTs onto this RH map.  Comparison of the map positions of zebrafish genes with their human orthologues helps reveal the correspondence between the zebrafish and human genomes.  We anticipate that such a comparison will aid gene identification and function in both human and zebrafish, and assist in reconstructing the evolutionary history of the vertebrate genome.


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