RepeatProfiler: A pipeline for visualization and comparative analysis of repetitive DNA profiles

Area of Science:

• Genomics
• Evolutionary Biology
• Bioinformatics

Background:

• Repetitive elements (REs) drive genome evolution and phenotypic change.
• REs offer insights into short-term evolutionary history due to their dynamic nature.
• Existing tools for RE analysis often require extensive genomic resources, limiting their use in non-model organisms.

Purpose of the Study:

• Introduce RepeatProfiler, a novel tool for analyzing repetitive DNA.
• Enable the generation, visualization, and comparison of repetitive element DNA profiles from low-coverage, short-read sequencing data.
• Facilitate evolutionary studies in diverse, non-model organisms with limited genomic resources.

Main Methods:

• Automated generation and visualization of repetitive element coverage depth profiles (RE profiles).
• Statistical comparison of RE profile shapes across multiple samples.
• Extraction and phylogenetic analysis of sequence variants within RE profiles as molecular characters.

Main Results:

• RepeatProfiler successfully generates and compares RE profiles from diverse datasets.
• The tool demonstrates utility in analyzing repetitive DNA in ground beetles, flies, and tomatoes.
• RE profiles provide a high-resolution data source for evolutionary insights.

Conclusions:

• RepeatProfiler is a valuable tool for studying repetitive DNA in various organisms.
• The method enhances comparative genomics and repeat biology research.
• It offers a powerful approach for species delimitation and understanding genome evolution.