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

Kristy B. Lidie^1,2, James C. Ryan², and Frances M. Van Dolah^1,2

¹ Marine Biomedicine and Environmental Sciences Center, Medical University of South Carolina, Charleston, SC

² Marine Biotoxins Program, NOAA Center for Coastal Environmental Health and Biomolecular Research, Charleston, SC

Karenia brevis is a dinoflagellate responsible for toxic red tides in the Gulf of Mexico. Although the mechanisms regulating its growth and toxicity are of considerable interest, little information is available on its molecular biology.  We therefore constructed a cDNA library to gain insight into its expressed genome and to develop tools for gene expression studies. Large scale sequencing yielded 7,001 ESTs representing 5,280 unigene clusters.  The vast majority of ESTs fall into a low-abundance class, with the highest expressed gene accounting for only 1% of all ESTs.  Approximately 29% of genes have similarity to known sequences in GenBank after BLASTx comparisons, p-value cut-off of 10e^-4.  We identify for the first time in a dinoflagellate a suite of conserved 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 copies. The ESTs were used to design a 60-mer oligonucleotide microarray.  Microarray labeling has been optimized and the microarray has been validated for probe specificity and reproducibility.  This is the first information on the expressed genome of a harmful algal species and provides the basis from which to begin functional genomic studies.