Genetic variability in Gymnodiniaceae ITS regions: implications for species identification and phylogenetic analysis

Abstract

The internal transcribed spacer (ITS) regions and 5.8S rRNA genes from several strains of toxic Gymnodiniaceae were sequenced and subjected to phylogenetic analysis with other Gymnodiniaceae species. Sequence comparisons showed that high sequence divergence existed in Gymnodiniaceae, especially in the genus Gymnodinium. The amplicons of the ITS regions from Amphidinium and Gyrodinium species were 438-439 and 604-605 bp, respectively, and those of the Gymnodinium species ranged from 575 to 615 bp. The mean distance value within Gymnodinium, calculated from the ITS sequence, was 0.68827 (range: 0-0.92323), 0.11342 for Amphidinium (range: 0.00467-0.17120) and 0.2005 for Karenia (range: 0.00521-0.29971). Low distance values were found within the species Gyrodinium instriatum (<0.01) and Karlodinium micrum (<0.02). Amphidinium remarkably had a shorter ITS than did other genera in Gymnodiniaceae, this implied that Amphidinium might be distant from the other Gymnodiniaceae and supported Saunders' opinion that the taxonomy of Amphidinium needs to be reevaluated. Largely congruent phylogenetic trees were produced by the maximum-parsimony method (PAUP), maximum-likelihood method (PAUP) and Bayesian inference (MrBayes), whereas the three analyses showed that the genera Gymnodinium and Karenia are unresolved groups in phylogeny. Minor sequence divergence was found within the different clones of Amphidinium carterae, suggesting that the ITS regions are suitable as genus- and species-specific oligonucleotide probes to rapidly detect and identify the red tide-forming algal species.