Article ID | Journal | Published Year | Pages | File Type |
---|---|---|---|---|
8644423 | Gene | 2018 | 33 Pages |
Abstract
Highly conserved 18S rDNA sequences encode ribosomal RNA and evolve in a concerted manner. In this study, 178 sequences of 18S rDNA from the ridge-eyed flounder, Pleuronichthys cornutus, were analyzed. The total sequences yielded five distinguishable types of 18S rDNA-A, B, R, S, and L-that were defined based on sequence alignments, clone clustering, and recombination detection. The length of 176 clones ranged from 1838â¯bp to 1846â¯bp, with one particularly short clone reaching only 1466â¯bp and one long clone reaching up to1869â¯bp. As per current criteria for pseudogene inference, Type S was inferred to be a pseudogene due to its truncated length (380â¯bp) and low minimum free energy (â536.9â¯kcal·molâ1). Type L had a unique 20-bp insertion and was also predicted to be as a pseudogene. Types A and B showed 31 differential sites, which in Type A was consistent with 18S rDNA sequences found in six other flounders, while Type B and recombinant Type R were not. Maximum K2P genetic distances were calculated within Type B (0.0232) and R (0.0313); these were much higher than that of Type A (0.0093) or between the six flounders (0.011). Only Type A was detected by reverse transcription experiments and linked to functional ITS1 and 5.8S fragments; Types B and R were linked to both functional and pseudo genes. Accordingly, Type A is likely the functional gene, and Types B and R are probable pseudogenes. The heterogeneity of the five types revealed that 18S rDNA sequences evolved in a non-concerted evolution manner in P. cornutus. Furthermore, our results suggest that more features should be used to identify functional or pseudo genes.
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Genetics
Authors
Min Yang, Xiaoyu Kong, Wei Shi, Li Gong, Hairong Luo, Baosheng Wu,