Intra-individual variation and transcribed pseudogenes in the ribosomal ITS1-5.8S-ITS2 rDNA of Paraplagusia japonica (Pleuronectiformes: Cynoglossidae).

The eukaryotic ribosomal DNA (rDNA) cluster consists of multiple copies of three genes (18S, 5.8S, and 28S rDNA) and two internal transcribed spacers (ITS1 and ITS2). Typically, rDNA is thought to be evolved in a strict concerted evolution pattern, in which show little or even no variations within species, while sequence diversity between species or higher taxa. However, in the present study, we reported a high level of intra-individual polymorphism of ITS1-5.8S-ITS2 rDNA in the genome of Paraplagusia japonica (Pleuronectiformes: Cynoglossidae), suggesting it conformed a non-concerted evolutionary pattern. Three divergent type sequences (Type A, B, and C) differing in length, GC content, secondary structure stability and minimum free energy coexisted in the genome of each studied individual. According to the particular features of ribosomal pseudogenes, Type B and Type C sequences were postulated as pseudogenes. Expression analyses gave clear evidence that both the functional gene and pseudogenes were abundantly transcribed, indicating expression is not an applicable criterion for identifying ribosomal pseudogenes. These findings will enrich useful data for the studies on rDNA evolution in flatfishes, as well as provide fresh insight on the transcribed ribosomal pseudogenes and further consideration of the definition of ribosomal pseudogene.