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ARPEGGIO: Automated Reproducible Polyploid EpiGenetic GuIdance workflOw
Stefan Milosavljevic1,2, Tony Kuo3, Samuele Decarli4
1Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
BMC Genomics
|July 18, 2021
Summary
ARPEGGIO is a new workflow for analyzing DNA methylation in polyploid species. It simplifies complex data analysis, improving the study of whole genome duplication events and their epigenetic impacts.
Area of Science:
- Genomics
- Epigenetics
- Evolutionary Biology
Background:
- Whole genome duplication (WGD) is a significant evolutionary force.
- DNA methylation plays a crucial role in the adaptation of polyploids.
- Analyzing polyploid epigenetics is challenging due to genomic complexity and data analysis burdens.
Purpose of the Study:
- To develop the first automated and reproducible workflow for analyzing epigenetic data in polyploids.
- To address the challenges of analyzing whole genome bisulfite sequencing (WGBS) data in allopolyploids.
- To facilitate a deeper understanding of DNA methylation's role in polyploid evolution.
Main Methods:
- Developed ARPEGGIO (Automated Reproducible Polyploid EpiGenetic GuIdance workflOw).
- Utilized an updated read classification algorithm (EAGLE-RC) to handle high sequence similarity in parental genomes.
- Integrated a comprehensive suite of analyses from raw WGBS data to differential methylation identification.
Main Results:
- EAGLE-RC demonstrated a 3-4 fold decrease in error rates compared to standard methods.
- ARPEGGIO outputs showed agreement with previously published results.
- ARPEGGIO is the only available workflow specifically designed for polyploid epigenetic data analysis.
Conclusions:
- ARPEGGIO promotes and supports polyploid research through automated and reproducible analyses.
- The workflow provides a convenient implementation for studying epigenetic variations in polyploids.
- ARPEGGIO is publicly available to advance the field of polyploid epigenetics.
