NDLI: Gene Expression in Florida Red Tide Dinoflagellate Karenia brevis: Analysis of an Expressed Sequence Tag Library and Development of DNA Microarray

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Gene Expression in Florida Red Tide Dinoflagellate Karenia brevis: Analysis of an Expressed Sequence Tag Library and Development of DNA Microarray

Content Provider	Springer Nature Link
Author	Lidie, Kristy B. Ryan, James C. Barbier, Michele Dolah, Frances M.
Copyright Year	2005
Abstract	Karenia brevis (Davis) is the dinoflagellate responsible for nearly annual red tides in the Gulf of Mexico. Although the mechanisms regulating the growth and toxicity of this problematic organism are of considerable interest, little information is available on its molecular biology. We therefore constructed a complementary DNA library from which to gain insight into its expressed genome and to develop tools for studying its gene expression. Large-scale sequencing yielded 7001 high-quality expressed sequence tags (ESTs), which clustered into 5280 unique gene groups. The vast majority of genes expressed fell into a low-abundance class, with the highest expressed gene accounting for only 1% of the total ESTs. Approximately 29% of genes were found to have similarity to known sequences in other organisms after BLAST similarity comparisons to the GenBank public protein database using a cutoff of P < 10e−4. We identified for the first time in a dinoflagellate a suite of conserved eukaryotic genes involved in cell cycle control, intracellular signaling, and the transcription and translation machinery. At least 40% of gene clusters displayed single nucleotide polymorphisms, suggesting the presence of multiple gene copies. The average GC content of ESTs was 51%, with a slight preference for G or C in the third codon position (53.5%). The ESTs were used to develop an oligonucleotide microarray containing 4629 unique features and 3462 replicate probes. Microarray labeling has been optimized, and the microarray has been validated for probe specificity and reproducibility. This is the first information to be developed on the expressed genome of K. brevis and provides the basis from which to begin functional genomic studies on this harmful algal bloom species.
Starting Page	481
Ending Page	493
Page Count	13
File Format	PDF
ISSN	14362228
Journal	Marine Biotechnology
Volume Number	7
Issue Number	5
e-ISSN	14362236
Language	English
Publisher	Springer-Verlag
Publisher Date	2005-06-15
Publisher Place	New York
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Karenia brevis dinoflagellate expressed sequence tag microarray Florida red tide functional genomics Oceanography
Content Type	Text
Resource Type	Article
Subject	Aquatic Science Biotechnology

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Preparation and Analysis of an Expressed Sequence Tag Library from the Toxic Dinoflagellate Alexandrium catenella

Characterization and Localization of a Hybrid Non-ribosomal Peptide Synthetase and Polyketide Synthase Gene from the Toxic Dinoflagellate Karenia brevis

Chimeric Plastid Proteome in the Florida “Red Tide” Dinoflagellate Karenia brevis

Exposure to the Florida red tide dinoflagellate, Karenia brevis, and its associated brevetoxins induces ecophysiological and proteomic alterations in Porites astreoides

Transcriptomic response of the red tide dinoflagellate, Karenia brevis, to nitrogen and phosphorus depletion and addition

Transcriptomic response of the red tide dinoflagellate, Karenia brevis, to nitrogen and phosphorus depletion and addition

Lessening the Hazards of Florida Red Tides: A Common Sense Approach

Analysis of Expressed Sequence Tags from the Harmful Alga, Prymnesium parvum (Prymnesiophyceae, Haptophyta)

Effects of the red tide dinoflagellate, Karenia brevis, on grazing and fecundity in the copepod Acartia tonsa

Gene Expression in Florida Red Tide Dinoflagellate Karenia brevis: Analysis of an Expressed Sequence Tag Library and Development of DNA Microarray

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Gene Expression in Florida Red Tide Dinoflagellate Karenia brevis: Analysis of an Expressed Sequence Tag Library and Development of DNA Microarray