Trematode and monogenean rRNA ITS2 secondary structures support a four-domain model

Area of Science:

• Molecular Biology
• Evolutionary Biology
• Parasitology

Background:

• The internal transcribed spacer 2 (ITS2) of ribosomal DNA (rDNA) plays a crucial role in ribosomal biogenesis.
• ITS2 sequences in trematodes are typically poorly conserved, hindering phylogenetic comparisons at higher taxonomic levels.
• Identifying conserved secondary structures within ITS2 can provide a framework for improving primary sequence alignments.

Purpose of the Study:

• To investigate the secondary structure of ITS2 sequences across various trematode species.
• To determine if conserved secondary structures can facilitate reliable phylogenetic analysis of trematodes.
• To identify conserved sequence elements within the ITS2 secondary structure.

Main Methods:

• Comparative analysis of ITS2 sequences from 39 trematode and one monogenean species.
• Secondary structure prediction and folding analysis.
• Alignment of sequences guided by predicted secondary structures.
• Phylogenetic tree construction based on aligned sequences.

Main Results:

• A conserved four-domain secondary structure model was predicted for trematode ITS2.
• Specific folding patterns were identified for different domains, with variations at the apex of domain B and across domains C and D.
• Conserved sequence strings were found in domains B and C, with potential functional or processing site significance.
• Phylogenetic analysis using secondary structure-guided alignment successfully distinguished the four recognized trematode orders.

Conclusions:

• Conserved secondary structures in trematode ITS2 provide a robust basis for phylogenetic analysis.
• The identified conserved regions and structural motifs are resistant to change, aiding evolutionary studies.
• Secondary structure information enhances the accuracy of phylogenetic reconstructions for trematodes.