ARPEGGIO

ARPEGGIO analyzes whole genome bisulfite sequencing (WGBS) data from allopolyploid species to classify reads by parental origin and identify differentially methylated genes associated with whole genome duplication (WGD) and polyploid evolution.

Key Features:

• Automated workflow: Implemented with Snakemake to execute WGBS processing steps from raw reads to final analyses.
• Comprehensive WGBS processing: Includes trimming, quality checks, alignment, methylation extraction, statistical analyses, and downstream analyses.
• Read classification (EAGLE-RC): Integrates the EAGLE-RC algorithm to classify reads against parental genome assemblies and address sequence similarity in allopolyploids.
• Differential methylation analysis: Performs statistical identification of differentially methylated genes from extracted methylation levels.
• Support for allopolyploid genomes: Explicitly handles sequence similarity between parental genomes during alignment and read assignment for polyploid-specific WGBS analysis.

Scientific Applications:

• Epigenetic responses to WGD: Detects DNA methylation changes following whole genome duplication events.
• Allopolyploid adaptation and stability: Investigates the role of DNA methylation in survival, adaptation, and stability of newly formed allopolyploids.
• Comparative epigenomics in polyploids: Enables comparison of methylation patterns between parental subgenomes to study polyploid evolution.

Methodology:

Raw WGBS reads undergo trimming and quality checks, are aligned to parental genome assemblies, are classified by parental origin using EAGLE-RC, have methylation levels extracted, and are subjected to statistical analyses to identify differentially methylated genes.