Development and experimental validation of a 20K Atlantic cod (Gadus morhua) oligonucleotide microarray based on a collection of over 150,000 ESTs

Autor: Stewart C. Johnson, Tudor Borza, Charles Y. Feng, Marije Booman, A. Kurt Gamperl, Jennifer Kimball, Rodney J. Ouellette, Anissa Belkaid, Adrian S. Culf, Ian C. Chute, Matthew L. Rise, Sharen Bowman, Tiago S. Hori, Sophie Hubert, Daniel Leger, Brent Higgins, Marlies Rise
Rok vydání: 2010
Předmět:
Genomics
Computational biology
Aeromonas salmonicida
Aquaculture
Aquatic Science
Microarray
Real-Time Polymerase Chain Reaction
Applied Microbiology and Biotechnology
Mass Spectrometry
03 medical and health sciences
Gadus
Animals
Nodaviridae
14. Life underwater
030304 developmental biology
DNA Primers
Gene Library
Oligonucleotide Array Sequence Analysis
Expressed Sequence Tags
0303 health sciences
Expressed sequence tag
biology
cDNA library
Reverse Transcriptase Polymerase Chain Reaction
Gene Expression Profiling
04 agricultural and veterinary sciences
biology.organism_classification
Molecular biology
Immunity
Innate
Gene expression profiling
Gadus morhua
Suppression subtractive hybridization
Atlantic cod
040102 fisheries
0401 agriculture
forestry
and fisheries
Original Article
Oligonucleotide Probes
Functional genomics
Spleen
Biotechnology
Zdroj: Marine Biotechnology (New York, N.y.)
Booman, M, Borza, T, Feng, C Y, Hori, T S, Higgins, B, Culf, A, Léger, D, Chute, I C, Belkaid, A, Rise, M, Gamperl, A K, Hubert, S, Kimball, J, Ouellette, R J, Johnson, S C, Bowman, S & Rise, M L 2011, ' Development and experimental validation of a 20K Atlantic cod (Gadus morhua) oligonucleotide microarray based on a collection of over 150,000 ESTs ', Marine Biotechnology, vol. 13, no. 4, pp. 733-50 . https://doi.org/10.1007/s10126-010-9335-6
ISSN: 1436-2236
Popis: The collapse of Atlantic cod (Gadus morhua) wild populations strongly impacted the Atlantic cod fishery and led to the development of cod aquaculture. In order to improve aquaculture and broodstock quality, we need to gain knowledge of genes and pathways involved in Atlantic cod responses to pathogens and other stressors. The Atlantic Cod Genomics and Broodstock Development Project has generated over 150,000 expressed sequence tags from 42 cDNA libraries representing various tissues, developmental stages, and stimuli. We used this resource to develop an Atlantic cod oligonucleotide microarray containing 20,000 unique probes. Selection of sequences from the full range of cDNA libraries enables application of the microarray for a broad spectrum of Atlantic cod functional genomics studies. We included sequences that were highly abundant in suppression subtractive hybridization (SSH) libraries, which were enriched for transcripts responsive to pathogens or other stressors. These sequences represent genes that potentially play an important role in stress and/or immune responses, making the microarray particularly useful for studies of Atlantic cod gene expression responses to immune stimuli and other stressors. To demonstrate its value, we used the microarray to analyze the Atlantic cod spleen response to stimulation with formalin-killed, atypical Aeromonas salmonicida, resulting in a gene expression profile that indicates a strong innate immune response. These results were further validated by quantitative PCR analysis and comparison to results from previous analysis of an SSH library. This study shows that the Atlantic cod 20K oligonucleotide microarray is a valuable new tool for Atlantic cod functional genomics research. Electronic supplementary material The online version of this article (doi:10.1007/s10126-010-9335-6) contains supplementary material, which is available to authorized users.
Databáze: OpenAIRE
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