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Updated: Jun 22, 2026
16:17
The ITS2 Database
Published on: March 12, 2012
ITS2 sequence-structure analysis in phylogenetics: a how-to manual for molecular systematics.
1Department of Bioinformatics, Biocenter, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany.
Molecular Phylogenetics and Evolution
|June 3, 2009
Summary
This review presents a flowchart for reliable phylogenetic tree estimation using nuclear ribosomal internal transcribed spacer 2 (ITS2) secondary structure. Compensatory base changes (CBCs) in ITS2 are proposed as a species-distinguishing marker.
Area of Science:
- Molecular Biology
- Bioinformatics
- Phylogenetics
Background:
- The nuclear ribosomal internal transcribed spacer 2 (ITS2) contains substantial phylogenetic information.
- Current studies often use ITS2 data inconsistently or inappropriately, leading to unreliable results.
Purpose of the Study:
- To introduce a standardized flowchart for estimating structure-based phylogenetic trees from ITS2 data.
- To highlight the utility of ITS2 secondary structure in phylogenetic analyses.
Main Methods:
- A pipeline utilizing the ITS2 Database, 4SALE, CBCAnalyzer, and ProfDistS was detailed.
- The method integrates ITS2 sequence and secondary structure information.
- An ITS2-specific scoring matrix and substitution model were employed.
Main Results:
- Phylogenetic trees derived from ITS2 structure-based methods are more reliable than those based on primary sequence data alone.
- Compensatory base changes (CBCs) within ITS2 sequence-structure pairs were identified.
Conclusions:
- The proposed flowchart provides a robust framework for ITS2-based phylogenetic analysis.
- ITS2 compensatory base changes (CBCs) show potential as a marker for species delimitation.
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