Marked intra-genomic variation and pseudogenes in the ITS1-5.8S-ITS2 rDNA of Symphurus plagiusa (Pleuronectiformes: Cynoglossidae)

in Animal Biology
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Abstract

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). In recent years, an increasing number of rDNA sequence polymorphisms have been identified in numerous species. In the present study, we provide 33 complete ITS (ITS1-5.8S-ITS2) sequences from two Symphurus plagiusa individuals. To the best of our knowledge, these sequences are the first detailed information on ITS sequences in Pleuronectiformes. Here, two divergent types (Type A and B) of the ITS1-5.8S-ITS2 rDNA sequence were found, which mainly differ in sequence length, GC content, nucleotide diversity (π), secondary structure and minimum free energy. The ITS1-5.8S-ITS2 rDNA sequence of Type B was speculated to be a putative pseudogene according to pseudogene identification criteria. Cluster analysis showed that sequences from the same type clustered into one group and two major groups were formed. The high degree of ITS1-5.8S-ITS2 sequence polymorphism at the intra-specific level indicated that the S. plagiusa genome has evolved in a non-concerted evolutionary manner. These results not only provide useful data for ribosomal pseudogene identification, but also further contribute to the study of rDNA evolution in teleostean genomes.

Marked intra-genomic variation and pseudogenes in the ITS1-5.8S-ITS2 rDNA of Symphurus plagiusa (Pleuronectiformes: Cynoglossidae)

in Animal Biology

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Figures

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    Alignment of two types of ITS1-5.8S-ITS2 rDNA sequences in S. plagiusa. The boundaries are marked by arrows. The dots indicate nucleotide identity to the top sequence and dashes indicate alignment gaps.

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    Nucleotide diversity of different types of ITS1-5.8S-ITS2 sequences in S. plagiusa.

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    Inferred secondary structures of two types of rDNA sequences in S. plagiusa. (A, B) ITS1 of Type A and Type B; (C, D) 5.8S of Type A and Type B; (E, F) ITS2 of Type A and Type B.

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    Maximum likelihood (ML) tree based on the ITS1-5.8S-ITS2 rDNA dataset (1000 bootstrap replicates). Bootstrap support values for maximum likelihood above the branch and Bayesian posterior probabilities below the branch.

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