Identification, Characterization, and Mapping of Expressed Sequence Tags from an Embryonic Zebrafish Heart cDNA Library
- Christopher Ton1,
- David M. Hwang1,
- Adam A. Dempsey1,
- Hong-Chang Tang1,
- Jennifer Yoon1,
- Mindy Lim1,
- John D. Mably2,
- Mark C. Fishman2, and
- Choong-Chin Liew1,3,4
- 1Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5G 1L5, Canada; 2Cardiovascular Research Center, Massachusetts General Hospital, Charlestown, Massachusetts 02129, USA and Department of Medicine, Harvard Medical School, Boston, Massachusetts 02115, USA; 3The Cardiovascular Genomic Unit, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA
Abstract
The generation of expressed sequence tags (ESTs) has proven to be a rapid and economical approach by which to identify and characterize expressed genes. We generated 5102 ESTs from a 3-d-old embryonic zebrafish heart cDNA library. Of these, 57.6% matched to known genes, 14.2% matched only to other ESTs, and 27.8% showed no match to any ESTs or known genes. Clustering of all ESTs identified 359 unique clusters comprising 1771 ESTs, whereas the remaining 3331 ESTs did not cluster. This estimates the number of unique genes identified in the data set to be approximately 3690. A total of 1242 unique known genes were used to analyze the gene expression patterns in the zebrafish embryonic heart. These were categorized into seven categories on the basis of gene function. The largest class of genes represented those involved in gene/protein expression (25.9% of known transcripts). This class was followed by genes involved in metabolism (18.7%), cell structure/motility (16.4%), cell signaling and communication (9.6%), cell/organism defense (7.1%), and cell division (4.4%). Unclassified genes constituted the remaining 17.91%. Radiation hybrid mapping was performed for 102 ESTs and comparison of map positions between zebrafish and human identified new synteny groups. Continued comparative analysis will be useful in defining the boundaries of conserved chromosome segments between zebrafish and humans, which will facilitate the transfer of genetic information between the two organisms and improve our understanding of vertebrate evolution.
[The sequence data described in this paper have been submitted to the GenBank data library under accession nos.BE693120–BE693210 and BE704450.]
Footnotes
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↵4 Corresponding author.
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E-MAIL cliew{at}rics.bwh.harvard.edu; FAX (617) 975-0995.
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Article and publication are at www.genome.org/cgi/doi/10.1101/gr.154000.
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- Received June 30, 2000.
- Accepted October 10, 2000.
- Cold Spring Harbor Laboratory Press
