Methylation data from Pseudotaxus chienii obtained using methylation-dependent restriction-site associated DNA...

Area of Science:

• Plant genetics and epigenetics
• Conservation biology
• Environmental adaptation

Background:

• Pseudotaxus chienii is an endangered, endemic Chinese conifer with limited adaptive capacity due to its sessile nature and long life cycle.
• Phenotypic variation, such as leaf size, exists along environmental gradients, suggesting potential adaptation mechanisms.
• DNA methylation is a key epigenetic mechanism that can influence phenotypic plasticity and adaptation in plants.

Purpose of the Study:

• To investigate the role of DNA methylation in driving phenotypic variation in Pseudotaxus chienii.
• To explore the methylation status of P. chienii individuals from diverse ecological niches.
• To provide insights into the epigenetic basis of adaptation in endangered plant species.

Main Methods:

• Employed methylation-dependent restriction-site associated DNA sequencing (MethylRAD) for a preliminary survey.
• Analyzed DNA methylation patterns in three Pseudotaxus chienii individuals from heterogeneous ecological niches.
• Quantified CCGG and CCHGG methylation tags to assess genome-wide methylation status.

Main Results:

• Generated a substantial number of high-quality methylation tags (372,611 CCGG and 726,332 CCHGG).
• Observed variation in methylation tag rates across different genomic sites (42.31%–50.18%).
• Found higher CCHGG methylation levels (16.63%) compared to CCGG (13.60%), potentially correlating with low phenotypic variation.

Conclusions:

• DNA methylation patterns, particularly the higher CCHGG methylation, may contribute to the observed low phenotypic variation in Pseudotaxus chienii.
• The findings suggest a potential epigenetic mechanism underlying the adaptation of this endangered species.
• Methylation data is publicly available in the Sequence Read Archive (SRA) database under accession SRP128155.