Intra-genomic variability and pseudogenes in ribosomal ITS regions of Paraplagusia blochii (Pleuronectiformes: Cynoglossidae)

Abstract

Abstract Eukaryotic nuclear ribosomal DNA (rDNA) typically evolves in a concerted manner, in which hundreds of rDNA sequences within species show little or no variations, whereas the sequences of different species diverge. There are few studies of the internal transcribed spacer regions (ITS1-5.8S-ITS2) in teleostean fishes and only one report on flatfishes. Here, we reported the discovery of two types of highly divergent ITS1-5.8S-ITS2 rDNA sequences (Type A and B) in the genome of the Bloch’s tonguesole, Paraplagusia blochii. These sequences mainly differ in sequence length, secondary structure, and minimum free energy. According to the potential features of pseudogenes, Type B sequences are speculated to be putative pseudogenic ITS regions. Cluster analyses also supported two major clades that corresponded to the sequence type. To the best of our knowledge, this is the first report of the ITS regions of tonguefish, and may therefore provide useful information for future studies of the rDNA of flatfishes as well as the patterns of rDNA evolution in teleostean fishes.