Structure-Based GC Investigation Sheds New Light on ITS2 Evolution in Corydalis Species

Guanine and cytosine (GC) content is a fundamental component of genetic diversity and essential for phylogenetic analyses. However, the GC content of the ribosomal internal transcribed spacer 2 (ITS2) remains unknown, despite the fact that ITS2 is a widely used phylogenetic marker. Here, the ITS2 wa...

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Bibliographic Details
Published in:International journal of molecular sciences 2023-04, Vol.24 (9), p.7716
Main Authors: Xian, Qing, Wang, Suyin, Liu, Yanyan, Kan, Shenglong, Zhang, Wei
Format: Article
Language:English
Subjects:
Base Pairing
Bias
Biological evolution
concerted evolution
Corydalis
Cytosine
DNA methylation
DNA, Ribosomal Spacer - genetics
Evolution
Evolution, Molecular
GC content
GC-biased evolution
Gene conversion
Genetic analysis
Genetic diversity
Genomes
Hypotheses
internal transcribed spacer 2
Mutation
Normal distribution
Phylogenetics
Phylogeny
Protein structure
Secondary structure
Structural stability
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Summary:Guanine and cytosine (GC) content is a fundamental component of genetic diversity and essential for phylogenetic analyses. However, the GC content of the ribosomal internal transcribed spacer 2 (ITS2) remains unknown, despite the fact that ITS2 is a widely used phylogenetic marker. Here, the ITS2 was high-throughput sequenced from 29 species, and their GC contents were comparatively investigated in the context of ITS2's characteristic secondary structure and concerted evolution. Our results showed that the GC contents of ITS2 were 131% higher than those of their adjacent 5.8S regions, suggesting that ITS2 underwent GC-biased evolution. These GCs were distributed in a heterogeneous manner in the ITS2 secondary structure, with the paired regions being 130% larger than the unpaired regions, indicating that GC is chosen for thermodynamic stability. In addition, species with homogeneous ITS2 sequences were always GC-rich, supporting GC-biased gene conversion (gBGC), which occurred with ITS2's concerted evolution. The RNA substitution model inferred also showed a GC preference among base pair transformations, which again supports gBGC. Overall, structurally based GC investigation reveals that ITS2 evolves under structural stability and gBGC selection, significantly increasing its GC content.
ISSN:1422-0067
1661-6596
1422-0067
DOI:10.3390/ijms24097716