Large subunit ribosomal RNA gene variation and sequence heterogeneity of Dinophysis (Dinophyceae) species from Scottish coastal waters

Abstract

The purpose of the study was to investigate the genetic diversity of Dinophysis species from around the Scottish coast, with a view to an improved understanding of the dynamics and identification of this genus in Scottish waters. Single-cell PCR amplification with direct sequencing was performed on a total of 441 Dinophysis cells isolated from both live and Lugol's fixed plankton net samples. Universal eukaryotic primers were used to amplify the large subunit (LSU) ribosomal RNA (rRNA) gene of the Dinophysis isolates, with a frequency of PCR success of 26% for non-fixed and 48% for fixed samples. From this a total of 30 isolates were selected for this study and the D1–D2 region of the LSU-rRNA gene sequenced for phylogenetic analysis. No significant correlation could be made between geographical location and LSU sequence, although some regional sequence heterogeneity was observed within the Dinophysis acuta species. LSU sequence data was used to design Dinophysis genus specific and Dinophysis clade-specific primers primarily to ensure clean sequences from universal D1–D2 amplicons without a requirement for cloning. Three clade-specific primers designed to a region within the D2 hypervariable region of the LSU-rRNA gene allowed discrimination of Dinophysis acuminata/ norvegica from Dinophysis tripos/caudata and Dinophysis fortii/ acuta. In two isolates, SC359 ( D. tripos) and LC58 ( D. acuta), nested PCR products were observed with both the expected clade-specific primer, and Dasd-R2, the D. acuminata/ norvegica clade-specific primer. Cloning and sequence analysis suggested that these amplicons were genuine “ D. acuminata-like” sequences and their presence, albeit at a low frequency within different Dinophysis species, indicated that individual Dinophysis cells possess heterologous copies of the LSU-rRNA gene that are similar to LSU sequences normally associated with D. acuminata. The nature of the process that generated these hybrid cells, the frequency of such events and their importance is as yet unknown, but may provide a cautionary note for the development of PCR-based species specific detection methods.