Development and Application of a Salmonid EST Database and cDNA Microarray: Data Mining and Interspecific Hybridization Characteristics

  1. Matthew L. Rise1,
  2. Kristian R. von Schalburg1,
  3. Gordon D. Brown1,
  4. Melanie A. Mawer1,
  5. Robert H. Devlin3,
  6. Nathanael Kuipers1,
  7. Maura Busby1,
  8. Marianne Beetz-Sargent1,
  9. Roberto Alberto1,
  10. A. Ross Gibbs1,
  11. Peter Hunt1,
  12. Robert Shukin4,
  13. Jeffrey A. Zeznik4,
  14. Colleen Nelson4,
  15. Simon R.M. Jones5,
  16. Duane E. Smailus6,
  17. Steven J.M. Jones6,
  18. Jacqueline E. Schein6,
  19. Marco A. Marra6,
  20. Yaron S.N. Butterfield6,
  21. Jeff M. Stott6,
  22. Siemon H.S. Ng2,
  23. William S. Davidson2, and
  24. Ben F. Koop1,7
  1. 1 Centre for Biomedical Research, University of Victoria, Victoria, British Columbia V8W 3N5 Canada
  2. 2 Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6 Canada
  3. 3 Aquaculture Division, Fisheries and Oceans Canada, West Vancouver, British Columbia V7V 1N6 Canada
  4. 4 Array Facility, Prostate Centre, Vancouver General Hospital, Vancouver, British Columbia V6H 3Z6 Canada
  5. 5 Pacific Biological Station, Fisheries and Oceans Canada, Nanaimo, British Columbia V9T 6N7 Canada
  6. 6 Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia V5Z 4E6 Canada

Abstract

We report 80,388 ESTs from 23 Atlantic salmon (Salmo salar) cDNA libraries (61,819 ESTs), 6 rainbow trout (Oncorhynchus mykiss) cDNA libraries (14,544 ESTs), 2 chinook salmon (Oncorhynchus tshawytscha) cDNA libraries (1317 ESTs), 2 sockeye salmon (Oncorhynchus nerka) cDNA libraries (1243 ESTs), and 2 lake whitefish (Coregonus clupeaformis) cDNA libraries (1465 ESTs). The majority of these are 3′ sequences, allowing discrimination between paralogs arising from a recent genome duplication in the salmonid lineage. Sequence assembly reveals 28,710 different S. salar, 8981 O. mykiss, 1085 O. tshawytscha, 520 O. nerka, and 1176 C. clupeaformis putative transcripts. We annotate the submitted portion of our EST database by molecular function. Higher- and lower-molecular-weight fractions of libraries are shown to contain distinct gene sets, and higher rates of gene discovery are associated with higher-molecular weight libraries. Pyloric caecum library group annotations indicate this organ may function in redox control and as a barrier against systemic uptake of xenobiotics. A microarray is described, containing 7356 salmonid elements representing 3557 different cDNAs. Analyses of cross-species hybridizations to this cDNA microarray indicate that this resource may be used for studies involving all salmonids.

Footnotes

  • [Supplemental material is available online at http://web.uvic.ca/cbr/grasp. The sequence data from this study have been submitted to GenBank dbEST under accession nos.: Salmo salar, BU965588–BU965906, CA036414–CA039704, CA039711–CA064598, CA767613–CA770910, and CB498694–CB518126; Oncorhynchus mykiss, CB485850–CB498693; Oncorhynchus tshawytscha, CB484816–CB485849; Oncorhynchus nerka, CD510521–CD511184; and Coregonus clupeaformis, CB483540–CB484653. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: C. Biagi, S. Dann, S. Temple, and R. Roper stimulated the S. salar head kidney cells used to create one cDNA library group.]

  • Article and publication are at http://www.genome.org/cgi/doi/10.1101/gr.1687304. Article published online before print in February 2004.

  • ↵7 Corresponding author. E-MAIL bkoop{at}uvic.ca; FAX (250) 472-4075.

    • Accepted December 12, 2003.
    • Received June 25, 2003.
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This Article

  1. Published in Advance February 12, 2004, doi: 10.1101/gr.1687304 Genome Res. 14: 478-490 Cold Spring Harbor Laboratory Press

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