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This study reveals DNA N⁶-methyladenine (6 mA) epigenetic marks in Riccia fluitans organellar genomes. Methylation patterns differ between aquatic and terrestrial forms, indicating a role in environmental adaptation for early land plants.

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Area of Science:

  • Plant epigenetics
  • Bryophyte genomics
  • Organellar DNA methylation

Background:

  • DNA N⁶-methyladenine (6 mA) is an emerging epigenetic mark in plants, crucial for transcriptional regulation and stress adaptation.
  • Its function in organellar genomes, particularly in early-diverging lineages, is not well understood.
  • The amphibious liverwort Riccia fluitans exhibits reversible morphotype changes between aquatic and terrestrial environments, making it ideal for studying epigenetic plasticity.

Purpose of the Study:

  • To investigate DNA N⁶-methyladenine (6 mA) methylation in the organellar genomes (plastid and mitochondrial) of Riccia fluitans.
  • To compare methylation patterns between aquatic and terrestrial morphotypes.
  • To explore the relationship between organellar methylation and gene expression in response to environmental conditions.

Main Methods:

  • Utilized Oxford Nanopore native DNA sequencing to profile 6 mA methylation across organellar genomes.
  • Integrated methylation data with Illumina RNA-seq gene expression profiles.
  • Cultivated Riccia fluitans under controlled aquatic and terrestrial conditions.

Main Results:

  • Identified habitat-specific 6 mA methylation sites in the organellar genomes of Riccia fluitans.
  • Observed a higher frequency of 6 mA methylation in the aquatic morphotype compared to the terrestrial one.
  • Found co-location of differentially expressed genes (e.g., accD, psbA) with environment-specific methylation sites, suggesting a link between methylation and gene expression.

Conclusions:

  • Provided the first genome-wide evidence of 6 mA methylation in the organellar genomes of Riccia fluitans.
  • Demonstrated that methylation patterns differ between aquatic and terrestrial forms, suggesting epigenetic regulation in environmental adaptation.
  • Highlighted a novel layer of epigenetic control in bryophytes, potentially contributing to adaptive plasticity in early land plants.