Journal
BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS
Volume 534, Issue -, Pages 233-239Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.bbrc.2020.11.106
Keywords
Ribosomal RNA; Tongue sole; Pseudogene; Non-concerted evolution; Internal transcribed spacer; Secondary structure
Categories
Funding
- Basic Scientific Research Operating Expenses of Zhejiang Provincial Universities [2019J00022]
- National Natural Science Foundation of China [41706176, 31471979]
- Natural Science Foundation of Zhejiang Province [LY21C190007]
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This study revealed a high level of intra-individual polymorphism of 18S-ITS1-5.8S rDNA in Cynoglossus melampetalus genome, indicating a non-concerted evolution manner. The presence of multiple types of rDNA sequences with differences in length, GC content, secondary structure stability, and minimum free energy challenges the previous assumption of homogeneity within species.
Many early studies of ribosomal RNA gene (rDNA) suggested that rDNA tandem repeats within species are homogeneous. However, increasing number of reports have found intra-individual rDNA polymorphism across a range of taxa. Here, we reported a high level of intra-individual polymorphism of 18S-ITS1-5.8S rDNA in the genome of Cynoglossus melampetalus (Pleuronectiformes: Cynoglossidae), indicating a non-concerted evolution manner. Sequence alignments found two distinct types of 18S and 5.8S (Type A and B) and five types of ITS1 sequence (Type A - E) coexisted in the genome differing in length, GC content, secondary structure stability and minimum free energy. Based on the unique features of pseudogene and comparison of the conserved 18S rDNA sequence and 5.8S secondary structure of 22 flatfishes revealed that Type B sequences of 18S, 5.8S and their linked ITS1 were putative pseudogenes. So far, detection of rRNA pseudogenes from the multiple rDNA copies has been an intricate puzzle. Our results, as a result, provide a new ideal for rRNA pseudogene identification. (C) 2020 Elsevier Inc. All rights reserved.
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