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

Abstract 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.