The ITS2 Database II: homology modelling RNA structure for molecular systematics

Area of Science:

• Molecular Biology
• Bioinformatics
• Phylogenetics

Background:

• The internal transcribed spacer 2 (ITS2) is increasingly used in phylogenetic analyses, primarily leveraging its fast-evolving sequence for low-level studies.
• Its conserved structural features also hold potential for higher-level phylogenies and species differentiation.
• Standard RNA folding algorithms often fail to accurately predict ITS2 structures, limiting its broader application.

Purpose of the Study:

• To develop and present a homology modeling approach for predicting RNA structures, specifically applied to the ITS2.
• To establish and describe the ITS2 Database, which houses predicted ITS2 structures.
• To overcome limitations in accurately determining ITS2 RNA structures for wider phylogenetic and taxonomic use.

Main Methods:

• Development of a homology modeling approach for RNA structure prediction.
• Application of the developed algorithms to predict ITS2 structures for a large dataset.
• Integration of predicted structures into the ITS2 Database.

Main Results:

• Successfully predicted the structures for 86,784 ITS2 sequences, representing over 55% of GenBank entries.
• Demonstrated that structure prediction is not uniformly distributed across genera, with some showing high prediction rates and others none.
• Identified potential for ITS2 structures diverging from the standard in certain genera.

Conclusions:

• The developed homology modeling approach significantly enhances the ability to predict ITS2 RNA structures.
• The ITS2 Database provides a valuable resource for researchers, containing a large collection of predicted structures.
• The findings suggest evolutionary divergence in ITS2 structures among different genera, opening new avenues for research.