ITS2 Secondary Structure Improves Discrimination between Medicinal "Mu Tong" Species when Using DNA Barcoding

Area of Science:

• Molecular Biology
• Bioinformatics
• Plant Taxonomy

Background:

• DNA barcoding is crucial for species identification, but a standardized plant DNA marker remains elusive.
• The ITS2 RNA transcript is proposed as a core barcode for seed plants, yet faces challenges due to conserved or overly variable regions.

Purpose of the Study:

• To investigate the efficacy of ITS2 secondary structure in resolving plant species identification.
• To evaluate ITS2 as a reliable DNA barcode by incorporating structural information for enhanced discrimination.

Main Methods:

• Predicted ITS2 secondary structures using Mfold software.
• Aligned sequences and structures using MARNA, transforming structures into coded data for Maximum Parsimony (MP) analysis.
• Constructed phylogenetic trees using both nucleotide sequences and structure-aligned data.

Main Results:

• Identified a conserved four-helix folding type with shared motifs in ITS2 structures across diverse plant families.
• Structure alignment facilitated the resolution of ambiguous sequences, leading to a well-supported phylogenetic tree.
• Successfully identified distinct 'Mu tong' herb species using short ITS2 fragments and their secondary structures.

Conclusions:

• ITS2 secondary structure information significantly enhances species discrimination capabilities for DNA barcoding.
• This approach strengthens the potential of ITS2 as a robust and reliable DNA barcode for plant identification and phylogenetic studies.