2 DISTINCT SMALL-SUBUNIT RIBOSOMAL-RNA GENES IN THE NORTH-AMERICAN TOXIC DINOFLAGELLATE ALEXANDRIUM-FUNDYENSE (DINOPHYCEAE)

Two distinct small-subunit ribosomal RNA genes, termed the A gene and B gene, were detected in a clonal isolate of the toxic dinoflagellate, Alexandrium fundyense Balech. The two sequences, which occur in roughly a 1:1 ratio in polymerase chain reaction-amplified material, differ at approximately 40 positions scattered throughout the length of the molecule. Transcripts of the B sequence were not detected in total RNA extracts from nutrient-replete and ammonium-starved (sexually induced) cultures or nutrient-replete log-phase cultures harvested at 2-h intervals over a complete circadian cycle. Many of the position changes in the B gene deviate from universally and eukaryotic-conserved small-subunit rRNA sequences. In contrast, the A gene is expressed under all culture conditions tested and does not violate any conserved sequence positions. Thus, the B sequence is not represented by stable transcripts and is likely a pseudogene. The B gene may serve as a useful marker for fine-scale population and taxonomic analyses of some Alexandrium species.