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

Area of Science:

• Genetics
• Molecular Evolution
• Bioinformatics

Background:

• Guanine and cytosine (GC) content is crucial for genetic diversity and phylogenetic analysis.
• The GC content of the ribosomal internal transcribed spacer 2 (ITS2), a common phylogenetic marker, was previously unknown.
• Understanding ITS2 GC content is vital for accurate phylogenetic studies.

Purpose of the Study:

• To investigate the GC content of ITS2 across 29 Corydalis species.
• To explore the relationship between ITS2 secondary structure, concerted evolution, and GC content.
• To determine the evolutionary forces shaping ITS2 GC composition.

Main Methods:

• High-throughput sequencing of ITS2 from 29 Corydalis species.
• Comparative analysis of GC content in ITS2 and adjacent 5.8S regions.
• Investigation of GC distribution within ITS2 secondary structures.
• Application of RNA substitution models to infer evolutionary preferences.

Main Results:

• ITS2 exhibited 131% higher GC content compared to adjacent 5.8S regions, indicating GC-biased evolution.
• GCs were preferentially located in paired regions of the ITS2 secondary structure, suggesting a role in thermodynamic stability.
• Homogeneous ITS2 sequences were GC-rich, supporting the role of GC-biased gene conversion (gBGC) in concerted evolution.
• RNA substitution models confirmed a GC preference in base pair transformations, further supporting gBGC.

Conclusions:

• ITS2 evolves under selection for structural stability and gBGC, leading to elevated GC content.
• The study elucidates the evolutionary mechanisms driving GC content in ITS2.
• Findings enhance the reliability of ITS2 as a phylogenetic marker by accounting for its unique evolutionary dynamics.