Genome-wide, evolutionary, and stress-responsive landscape of the Pectin methylesterase gene family in cucumber and muskmelon

Pectin methylesterases (PMEs) are key regulators of plant cell wall remodeling; however, their evolutionary dynamics and stress-responsive roles remain poorly understood in cucurbit crops. This study aimed to systematically characterize the PME gene family in cucumber (Cucumis sativus) and muskmelon (Cucumis melo), addressing how PME diversification, duplication, and regulatory architecture underpin their responses to biotic and abiotic stresses. Using a Hidden Markov Model-based genome-wide screening approach, we identified 52 PME genes in cucumber and 56 in muskmelon, which were classified into Type I and Type II PMEs based on their domain composition. Comparative structural and phylogenetic analyses revealed conserved domain organization but substantial intron-driven structural diversification, resolving PMEs into two major evolutionary lineages with lineage-specific expansion patterns. Duplication and synteny analyses demonstrated that dispersed duplication was the primary driver of PME family expansion, while Ka/Ks estimates indicated strong purifying selection, highlighting functional conservation across cucurbits. Promoter cis-element profiling and protein-protein interaction network analyses revealed extensive enrichment of stress- and hormone-responsive regulatory features, identifying central PME hub genes. Meta-transcriptomic analyses across diverse biotic and abiotic stresses revealed dynamic, condition-specific PME regulation, with Type I PMEs predominantly associated with stress responses in cucumber, whereas both PME types contributed substantially in muskmelon. Several PMEs exhibited conserved stress-induced expression, while others displayed species-, tissue-, or pathogen-specific patterns. Collectively, this study establishes an integrative evolutionary and stress-responsive framework for PME genes in cucurbits, providing mechanistic insights into cell wall plasticity and identifying candidate PME targets for improving multi-stress resilience in crop breeding.