PhaeoEpiView

PhaeoEpiView provides an epigenome browser for Phaeodactylum tricornutum that integrates telomere-to-telomere genome assemblies, lifted Phatr3 gene models, DNA methylation, histone post-translational modification data, and transposable element annotations to support epigenomic analyses.

Key Features:

• Updated Genome Assembly: Uses a telomere-to-telomere genome assembly derived from long-read sequencing to provide a contiguous reference for epigenomic mapping.
• Lifted Gene Models: Incorporates gene models lifted from the Phatr3 reference to reconcile annotations with the new assembly.
• Epigenome Mapping: Maps DNA methylation and histone post-translational modifications onto the updated assembly, including annotations for transposable elements.
• Enhanced Histone Mark Data: Reprocesses previously published histone ChIP data with improved peak calling and uses deeper sequencing and monoclonal-antibody–based datasets to increase mark precision.
• Transposable Element Annotations: Integrates newly published transposable element annotations for comprehensive epigenomic context.

Scientific Applications:

• Molecular environmental studies: Enables analysis of epigenetic responses of Phaeodactylum tricornutum to environmental conditions.
• Gene regulation research: Supports investigation of DNA methylation and histone modification roles in gene expression regulation.
• Transposable element biology: Facilitates study of epigenetic regulation and activity of transposable elements.
• Comparative epigenomics in stramenopiles: Provides a reference for comparative analyses of epigenomic features across stramenopile species.

Methodology:

Gene models were lifted from Phatr3 to the telomere-to-telomere assembly; DNA methylation and histone post-translational modifications were mapped to the new assembly; histone-mark peaks were called using improved peak calling methods and sequencing datasets (including long-read and deeper sequencing) were integrated.