The ITS2 Database.

Area of Science:

• Molecular Biology
• Bioinformatics
• Phylogenetics

Background:

• The internal transcribed spacer 2 (ITS2) is a widely used phylogenetic marker.
• Previous ITS2 research primarily focused on sequence variability, limiting its phylogenetic resolution.
• Incorporating ITS2 secondary structure significantly enhances phylogenetic inference across various taxonomic levels, including species delimitation.

Purpose of the Study:

• To present an exhaustive, reannotated dataset of ITS2 sequences and their secondary structures.
• To provide a comprehensive bioinformatics workbench for ITS2 data analysis and phylogenetic reconstruction.
• To facilitate both initial and large-scale phylogenetic analyses using ITS2 sequence-structure information.

Main Methods:

• Utilized profile Hidden Markov Models (HMMs) for accurate ITS2 sequence annotation.
• Employed minimum energy-based folding and homology modeling for predicting secondary structures.
• Integrated tools for sequence-structure alignment and phylogenetic tree reconstruction (e.g., 4SALE, ProfDistS, Neighbor Joining).

Main Results:

• The ITS2 Database offers a curated collection of ITS2 sequences with predicted secondary structures.
• The database provides integrated tools for annotation, structural prediction, motif detection, and BLAST searches.
• A complete analysis pipeline is available, simplifying the process from raw sequences to phylogenetic trees.

Conclusions:

• Combining ITS2 sequence and secondary structure data offers superior phylogenetic resolution compared to sequence data alone.
• The ITS2 Database serves as a valuable resource for researchers, simplifying and advancing phylogenetic studies.
• The integrated analysis pipeline streamlines complex bioinformatics workflows for ITS2-based phylogenetics.