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Related Experiment Video

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Genotyping Single Nucleotide Polymorphisms in the Mitochondrial Genome by Pyrosequencing

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Remarkable sequence polymorphisms in 18S rDNA of Pleuronichthys cornutus (Pleuronectiformes: Pleuronectidae).

Min Yang¹, Xiaoyu Kong², Wei Shi²

¹CAS Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou 510301, China; University of Chinese Academy of Sciences, Beijing 100049, China.

|July 29, 2018

Summary

Analysis of ridge-eyed flounder 18S rDNA revealed five types, with Type A likely functional and others pseudogenes. This suggests non-concerted evolution and the need for broader criteria to identify functional genes.

Keywords:

18S rDNA Non-concerted evolution Polymorphism Pseudogene Recombination

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Published on: April 1, 2019

Area of Science:

Molecular Biology
Genetics
Evolutionary Biology

Background:

Highly conserved 18S ribosomal DNA (rDNA) sequences are crucial for ribosomal RNA synthesis.
These sequences typically evolve in a concerted manner across related species.
Understanding 18S rDNA variation is key to studying gene evolution and function.

Purpose of the Study:

To analyze the diversity of 18S rDNA sequences in the ridge-eyed flounder (Pleuronichthys cornutus).
To identify potentially functional and pseudogene variants within the 18S rDNA locus.
To investigate the evolutionary dynamics of 18S rDNA in this species.

Main Methods:

Sequencing and analysis of 178 18S rDNA clones from P. cornutus.
Sequence alignment, clone clustering, and recombination detection to differentiate sequence types.
Pseudogene inference based on length, minimum free energy, and unique insertions.
Reverse transcription experiments to assess gene activity and linkage to functional fragments.

Main Results:

Five distinct 18S rDNA types (A, B, R, S, L) were identified.
Types S and L were inferred as pseudogenes due to truncated length and unique features.
Type A showed high similarity to other flounder 18S rDNA, while Type B and recombinant Type R exhibited higher genetic distances.
Reverse transcription confirmed Type A as the likely functional gene, linked to ITS1 and 5.8S fragments.

Conclusions:

18S rDNA sequences in P. cornutus evolved in a non-concerted manner, challenging previous assumptions.
Type A is identified as the functional 18S rDNA gene, while Types B, R, S, and L are likely pseudogenes.
The study highlights the need for comprehensive criteria beyond sequence length and energy to accurately distinguish functional genes from pseudogenes.