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PMID: 14962987 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

Development and application of a salmonid EST database and cDNA microarray: data mining and interspecific hybridization characteristics.

Genome research ·Vol. 14 ·No. 3 ·2004-03-00 ·Pages 478-90

Rise ML, von Schalburg KR, Brown GD, Mawer MA, Devlin RH, Kuipers N, Busby M, Beetz-Sargent M, Alberto R, Gibbs AR, Hunt P, Shukin R, Zeznik JA, Nelson C, Jones SR, Smailus DE, Jones SJ, Schein JE, Marra MA, Butterfield YS, Stott JM, Ng SH, Davidson WS, Koop BF

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.

MeSH Terms
Animals Computational Biology/methods Databases, Genetic Expressed Sequence Tags Gene Library Genes/genetics,physiology Genes, Duplicate/genetics Hybridization, Genetic/genetics Molecular Sequence Data Oligonucleotide Array Sequence Analysis/methods Oncorhynchus/genetics Oncorhynchus mykiss/genetics Organ Specificity/genetics,physiology Salmo salar/genetics Salmonidae/genetics Species Specificity
Authors & Affiliations
24 authors, click to expand affiliations / ORCID
Rise Matthew L
Centre for Biomedical Research, University of Victoria, Victoria, British Columbia V8W 3N5 Canada.
von Schalburg Kristian R
Brown Gordon D
Mawer Melanie A
Devlin Robert H
Kuipers Nathanael
Busby Maura
Beetz-Sargent Marianne
Alberto Roberto
Gibbs A Ross
Hunt Peter
Shukin Robert
Zeznik Jeffrey A
Nelson Colleen
Jones Simon R M
Smailus Duane E
Jones Steven J M
Schein Jacqueline E
Marra Marco A
Butterfield Yaron S N
Stott Jeff M
Ng Siemon H S
Davidson William S
Koop Ben F
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Article Info
Journal
Genome research
Abbr.
Genome Res
ISSN
1088-9051
DOI
10.1101/gr.1687304
Published
2004-03-00
Epub
2004-00-12
Pages
478-90
Language
English
Region
United States
NLM ID
9518021
PMCID
PMC353236
Subset
IM
Databases
GENBANK
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PubMed source DOI: 10.1101/gr.1687304 PMC Full Text View journal details
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