How drought and ploidy level shape gene expression and DNA methylation in Phragmites australis

Key drought-response genes regulate saccharopine, mevalonate, water-stress pathways, and cell wall remodeling. Ploidy level influences gene expression under drought and non-stress conditions. Octoploids overall exhibit lower methylation than tetraploids. Drought stress significantly affects plant physiology and growth, yet the molecular mechanisms underlying drought responses remain poorly understood. In this study, we investigate how tetraploid and octoploid Phragmites australis (common reed), a key species in wetland ecosystems and paludiculture, respond to drought at the transcriptional and epigenetic levels. Using RNA-seq, we identify changes in gene expression after 20 and 30 days of drought and assess methylation-sensitive amplification polymorphism (MSAP) over 50 days of drought. Transcriptomic analysis reveals that key drought-response genes are shared between ploidy levels, including those involved in the saccharopine pathway, water deprivation response, cell wall remodeling, and the mevalonate pathway. Drought suppresses photosynthetic genes, with PsbP downregulated by up to 32-fold. Ploidy level influences gene expression under both drought and non-stress conditions, highlighting distinct adaptive strategies. In control samples, gene expression differed between ploidy levels, with octoploids upregulating genes related to translation and metabolism, while tetraploids activate genes involved in cell wall modification and transmembrane transport. Prolonged drought increases DNA methylation variability, though no significant correlation was detected between methylation levels and drought duration. Methylation differences are more pronounced between ploidy levels, with octoploids exhibiting lower overall methylation. These findings highlight the complex interactions between gene expression, epigenetic modifications, and polyploidy in drought response and provide a theoretical framework for future selection, hybridization, and conservation initiatives.