Evaluation of the complete nuclear rDNA unit sequence of the jellyfish Cyanea nozakii Kishinouye (Scyphozoa: Semaeostomeae) for molecular discrimination

The harmful jellyfish Cyanea nozakii Kishinouye has frequently occurred on Korean coasts, and its blooms have caused serious ecological and economic damages. DNA sequences of the C. nozakii for molecular detection and discrimination are relatively scarce. In this study, we determined the complete sequence of a single unit of tandemly repeated ribosomal DNA (rDNA) of the Korean C. nozakii and characterized the molecular features of the rDNA. The complete rDNA contained 8,003 bp (48.4% GC) with the same gene arrangement (18S, ITS1, 5.8S, ITS2, 28S, and IGS) to the typical eukaryotes. Dot plot analysis showed that the coding regions (18S, 5.8S, and 28S) were highly conserved, while the non-coding regions (ITS1, ITS2, and IGS) were more variable and parsimony-informative. The IGS contained a putative transcription termination signal (poly(T) tract) and four repeats of block minisatellites. Phylogenetic analyses using 18S and 28S rDNA revealed well-resolved relationships of C. nozakii within the order Semaeostomeae, separating it from other Cyanea species. The complete rDNA sequence provides various options for the selection of jellyfish taxonomic markers and may be useful for discriminating between species of C. nozakii and phylogeny reconstruction with close relatives.