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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

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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.

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Acknowledgments

We thank Jeral Tyler and Bennie Haynes for laboratory assistance, Jeanine Miller-Morey for culture maintenance, and Paul Gross for use of the Qiagen Biobot 9600 system. EST sequencing was performed by Seqwright, Houston, Texas. Funding for this project was provided by NOAA programmatic funding for Marine Biotoxins and ECOHAB grants ECO-01-242 and NA03NOS478 to F.M.V.D.

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Author notes

  1. Michele Barbier

    Present address: Michele Barbier, Statione Biologique, Roscoff, France

Authors and Affiliations

  1. Marine Biotoxins Program, NOAA Center for Coastal Environmental Health and Biomolecular Research, 219 Fort Johnson Rd., Charleston, SC, 29412, U.S.A.

    Kristy B. Lidie, James C. Ryan, Michele Barbier & Frances M. Van Dolah

  2. Marine Biomedicine and Environmental Sciences, Medical University of South Carolina, Charleston, South Carolina, U.S.A.

    Kristy B. Lidie & Frances M. Van Dolah

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  1. Kristy B. Lidie
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  2. James C. Ryan
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  4. Frances M. Van Dolah
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Correspondence to Frances M. Van Dolah.

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Lidie, K.B., Ryan, J.C., Barbier, M. et al. Gene Expression in Florida Red Tide Dinoflagellate Karenia brevis: Analysis of an Expressed Sequence Tag Library and Development of DNA Microarray. Mar Biotechnol 7, 481–493 (2005). https://doi.org/10.1007/s10126-004-4110-6

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  • DOI: https://doi.org/10.1007/s10126-004-4110-6

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