TWO DISTINCT SMALL‐SUBUNIT RIBOSOMAL RNA GENES IN THE NORTH AMERICAN TOXIC DINOFLAGELLATE ALEXANDRIUM FUNDYENSE (DINOPHYCEAE)1

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Abstract
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.

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