Recombination and incomplete concerted evolution of the ribosomal 18S (partial) -ITS1-5.8S-ITS2-28S (partial) rDNA in Cynoglossus trigrammus genome

Abstract

Nuclear ribosomal RNA gene (nrDNA) has long been deemed as an archetypal example illustrating concerted evolution. However, nrDNA has been found to be polymorphic in an increasing number of species. The ribosomal internal transcribed spacer region (ITS1-5.8S-ITS2) is of great importance to molecular barcoding and phylogenetic studies, but it almost remains unknown in some large taxa of Pleuronectiformes (flatfish). In this study, the polymorphisms of the 18S (partial) -ITS1-5.8S-ITS2-28S (partial) rDNA sequence in two Cynoglossus trigrammus individuals were investigated using a PCR cloning approach. Four main types of rDNA sequences (Type A, R1, R2, and B) were found, indicating a consistent lack of homogeneity. This confirmed the existence of significant levels of variation within individuals in tonguefish (Cynoglossidae) genomes. Type A sequence was inferred to be a putative pseudogene because of its shorter length, lower minimum free energy, less stable secondary structure, and remarkable variations in the conserved regions. Type R1 and R2 sequences were detected as recombinants. The most likely turnover mechanism generating this variation pattern was gene conversion operating at the intra-chromosomal level. These results will not only provide useful information for polymorphism analysis of ribosomal RNA genes in flatfish, but also shed light on the complex dynamic evolution of rDNA in teleost genomes.