AlphaBeta

AlphaBeta estimates epimutation rates and spectra from high-throughput plant DNA methylation data to quantify spontaneous epimutations and their contributions to methylome diversity.

Key Features:

• Epimutation rate and spectrum estimation: AlphaBeta estimates spontaneous epimutation rates and spectra from high-throughput plant DNA methylation data.
• Pedigree-based analysis: It leverages pedigree-based DNA methylation datasets and mutation accumulation lines (MA-lines) to quantify epimutations across generations.
• Germline epimutation analysis: It analyzes germline epimutations within multi-generational MA-lines to assess heritable methylation changes transmitted through sexual reproduction.
• Somatic epimutation analysis: It quantifies somatic epimutations that accumulate during plant development and aging within individual plants.
• Support for clonal and sexual MA-lines and perennials: It has been demonstrated on clonal and sexually derived MA-lines and on long-lived perennial plants.
• Molecular clock utility: It detects neutral, genome-wide accumulation of spontaneous epimutations that can be used to age-date trees and other perennials.

Scientific Applications:

• Mutation accumulation studies: Provides precise estimates of epimutation rates and spectra to study accumulation of epimutations over generations.
• Developmental biology research: Enables analysis of somatic epimutations during plant development and aging to investigate molecular mechanisms of growth and senescence.
• Aging studies in perennials: Acts as a molecular clock to estimate the age of trees and other long-lived plants from genome-wide epimutation accumulation.

Methodology:

AlphaBeta processes high-throughput DNA methylation data by employing computational algorithms that quantify stochastic epimutation events and analyzes these changes within the context of plant pedigrees, including mutation accumulation lines.