Ribosomal ITS sequences and plant phylogenetic inference

Area of Science:

• Molecular Biology
• Phylogenetics
• Genomics

Background:

• The internal transcribed spacer (ITS) region of the nuclear ribosomal cistron is a prevalent marker for plant phylogenetic inference.
• A significant percentage of phylogenetic studies, particularly at the genus level, utilize ITS sequence data.

Purpose of the Study:

• To review molecular genetic processes impacting ITS sequences that may mislead phylogenetic inference.
• To highlight the mechanisms and phylogenetic implications of ITS sequence variation.
• To suggest alternative genetic markers for more reliable phylogenetic analysis.

Main Methods:

• Review of molecular genetic processes affecting ITS sequences.
• Analysis of phylogenetic publications utilizing ITS data.
• Comparison of homoplasy levels in ITS versus other DNA sequence datasets.

Main Results:

• ITS sequences exhibit extensive variation due to array duplication, pseudogenes, and incomplete homogenization.
• These variations create paralogous sequence relationships that can confound phylogenetic reconstruction.
• Homoplasy is higher in ITS compared to other DNA markers, likely due to orthology/paralogy conflation and alignment issues.

Conclusions:

• The complex and unpredictable evolutionary behavior of ITS sequences reduces their utility for accurate plant phylogenetic analysis.
• Alternative markers, such as single-copy or low-copy nuclear genes, are recommended for more robust phylogenetic insights.