DNA methylation dynamics in gymnosperm duplicate genes: implications for genome evolution and stress adaptation

Area of Science:

• Plant evolutionary genomics
• Epigenetics and transcriptional regulation
• Comparative genomics

Background:

• Duplicate genes drive evolutionary innovation, with expression divergence offering insights into DNA methylation's role.
• Previous research on DNA methylation in duplicate genes is limited to angiosperms, leaving major plant lineages understudied.

Purpose of the Study:

• To investigate DNA methylation evolution in duplicate genes across diverse gymnosperm species.
• To understand the relationship between DNA methylation, gene expression, and adaptation in long-lived plant lineages.

Main Methods:

• Analysis of genomic, transcriptomic, and high-depth DNA methylomic data from representative gymnosperm species.
• Examination of DNA methylation patterns along gene bodies, flanking regions, and coding regions.
• Correlation analysis between DNA methylation divergence and gene expression divergence.

Main Results:

• Observed variations in DNA methylation across gene structures and duplication types, with frequent biased divergence between duplicate copies.
• Methylation divergence in downstream regions negatively correlated with gene expression; CG and CHG methylation positively correlated with gene length.
• Duplicate genes with both methylation and expression divergence were enriched in adaptation-related processes, particularly stress response.

Conclusions:

• DNA methylation plays a significant role in regulating gene expression and facilitating adaptive evolution in gymnosperms.
• Epigenomic buffering via DNA methylation may mitigate gene length's impact on expression.
• DNA methylation, particularly CG and non-CG patterns in coding regions, can silence translocated duplicates, reducing genetic redundancy and aiding adaptation.