ARPEGGIO

ARPEGGIO processes whole-genome bisulfite sequencing (WGBS) data from allopolyploid species to classify reads against parent genome assemblies and produce methylation calls and differential methylation results using the EAGLE-RC classifier within a Snakemake workflow.

Key Features:

• Workflow management (Snakemake): Orchestrates automated execution of analysis steps including quality control, trimming, alignment, methylation extraction, and downstream analyses.
• Read classification (EAGLE-RC): Uses the EAGLE-RC algorithm to assign reads to parental subgenomes based on parent-species genome assemblies, addressing sequence similarity in allopolyploids.
• WGBS preprocessing and alignment: Performs quality assessment, adapter/quality trimming, and alignment of bisulfite-converted reads to parent genome assemblies.
• Methylation extraction: Extracts cytosine methylation levels from aligned reads to generate methylation calls.
• Differential methylation analysis: Applies statistical analyses to identify differentially methylated regions (DMRs) and genes.
• Validation and performance benchmarking: EAGLE-RC has been tested on publicly available datasets with known ground truth, reducing classification error rates by three- to four-fold compared to standard approaches.

Scientific Applications:

• Allopolyploid epigenetics: Resolve DNA methylation patterns in newly formed allopolyploids arising from hybridization and whole genome duplication (WGD).
• WGD impact on gene regulation: Identify genes with altered methylation to study links between epigenetic modification and gene expression following WGD.
• Comparative methylomics: Compare parental-subgenome methylation patterns to investigate epigenetic contributions to adaptation and phenotypic diversity in polyploids.

Methodology:

Implemented as a Snakemake workflow that performs quality assessment and trimming of raw WGBS reads, classifies and aligns reads to parent genome assemblies using EAGLE-RC, extracts methylation levels, and conducts statistical analyses to identify DMRs and genes with differential methylation.