Development and Application of a Salmonid EST Database and cDNA Microarray: Data Mining and Interspecific Hybridization Characteristics
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 EST...
Published in: | Genome Research |
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Main Authors: | , , , , , , , , , , , , , , , , , , , , , , , |
Format: | Text |
Language: | English |
Published: |
Cold Spring Harbor Laboratory Press
2004
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Subjects: | |
Online Access: | http://www.genome.org/cgi/content/short/1687304v1 https://doi.org/10.1101/gr.1687304 |
Summary: | 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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