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ITS secondary structure derived from comparative analysis: implications for sequence alignment and phylogeny of the
Leslie R Goertzen1, Jamie J Cannone, Robin R Gutell
1Section of Integrative Biology and Institute of Cellular and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA. goertzen@indiana.edu
Molecular Phylogenetics and Evolution
|September 19, 2003
Summary
A new RNA secondary structure model for the nuclear ribosomal internal transcribed spacers (ITS) in Asteraceae plants was developed. This model aids in understanding molecular evolution and constructing the first nuclear DNA-based family phylogeny for Asteraceae.
Area of Science:
- Molecular Biology
- Phylogenetics
- Bioinformatics
Background:
- The nuclear ribosomal internal transcribed spacers (ITS) are crucial non-coding DNA regions.
- Understanding ITS RNA secondary structure is vital for molecular evolutionary studies.
- Previous studies primarily used thermodynamic criteria to model ITS structures.
Purpose of the Study:
- To develop an RNA secondary structure model for the nuclear ribosomal ITS in the Asteraceae family.
- To provide a framework for broad-scale molecular evolutionary studies within Asteraceae.
- To construct the first family-level phylogeny of Asteraceae using nuclear DNA data.
Main Methods:
- Comparative analysis of 340 angiosperm sequences from the Asteraceae family.
- Covariation analysis to infer RNA secondary structure.
- Phylogenetic analysis using ITS sequence data and combined with ndhF sequences.
Main Results:
- A minimum structure model for ITS RNA was established, revealing significant base pairing in ITS1 (20%) and ITS2 (38%).
- The conserved structural features enabled accurate sequence alignment.
- The resulting ITS-based phylogeny showed high resolution and congruence with chloroplast DNA studies, supporting a monophyletic Asteroideae and paraphyletic Cichorioideae.
Conclusions:
- The RNA secondary structure model enhances understanding of ITS evolution in Asteraceae.
- Nuclear ITS DNA data provides a robust framework for Asteraceae phylogeny.
- Combined analyses of ITS and ndhF sequences offer improved resolution for family relationships.