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

Matthew L. Rise | Zendy; Kristian R. von Schalburg | Zendy; Gordon D. Brown | Zendy; Melanie A. Mawer | Zendy; Robert H. Devlin | Zendy; Nathanaël Kuipers | Zendy; Maura Busby | Zendy; Marianne Beetz-Sargent | Zendy; Roberto Alberto | Zendy; A. R. Gibbs | Zendy; Peter Hunt | Zendy; Robert Shukin | Zendy; Jeffrey A. Zeznik | Zendy; Colleen C. Nelson | Zendy; Simon R. M. Jones | Zendy; Duane E. Smailus | Zendy; Steven J.M. Jones | Zendy; Jacqueline E. Schein | Zendy; Marco A. Marra | Zendy; Yaron S.N. Butterfield | Zendy; Jeff Stott | Zendy; Siemon H. S. Ng | Zendy; William S. Davidson | Zendy; Ben F. Koop | Zendy

Open Access

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

Author(s) -

Matthew L. Rise,

Kristian R. von Schalburg,

Gordon D. Brown,

Melanie A. Mawer,

Robert H. Devlin,

Nathanaël Kuipers,

Maura Busby,

Marianne Beetz-Sargent,

Roberto Alberto,

A. R. Gibbs,

Peter Hunt,

Robert Shukin,

Jeffrey A. Zeznik,

Colleen C. Nelson,

Simon R. M. Jones,

Duane E. Smailus,

Steven J.M. Jones,

Jacqueline E. Schein,

Marco A. Marra,

Yaron S.N. Butterfield,

Jeff Stott,

Siemon H. S. Ng,

William S. Davidson,

Ben F. Koop

Publication year - 2004

Publication title -

genome research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.556

H-Index - 297

eISSN - 1549-5469

pISSN - 1088-9051

DOI - 10.1101/gr.1687304

Subject(s) - biology , expressed sequence tag , complementary dna , cdna library , salmo , oncorhynchus , rainbow trout , genetics , rapid amplification of cdna ends , microarray , gene , microbiology and biotechnology , gene expression , fishery , molecular cloning , fish <actinopterygii>

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.

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