Genome-Wide Identification of the ACE Gene Family in Melon (Cucumis melo L.) and Its Response to Autotoxicity and Saline-Alkali Stress

Soil salinization and autotoxicity are major abiotic stresses constraining melon production. The ACE gene family (also known as HOTHEAD, HTH) encodes flavin-containing oxidoreductases involved in stress responses and RNA cache-mediated non-Mendelian inheritance. This study presents a comprehensive genome-wide analysis of the ACE/HTH gene family in melon through integrated bioinformatic and experimental approaches. We identified 14 CmACE genes encoding proteins of 457–595 amino acids. This gene family underwent significant expansion through tandem duplication events, particularly on chromosome 5. Phylogenetic analysis grouped these genes into three distinct clades with conserved gene structures and motif compositions. Promoter analysis identified abundant stress- and hormone-responsive cis-elements, with ABRE elements being predominant. Expression analyses revealed that multiple CmACE genes, including CmACE3, CmACE5, CmACE6 and CmACE14, were significantly upregulated under salt-alkali and autotoxicity stresses, showing distinct tissue-specific and time-dependent expression patterns. Notably, CmACE3 and CmACE6 were strongly induced under both stresses, while the tandemly duplicated pair CmACE6 and CmACE7 exhibited divergent expression patterns, suggesting functional specialization. Our findings provide the first comprehensive characterization of the CmACE gene family in melon, revealing its evolutionary history and stress-responsive regulation. These results not only offer valuable genetic resources for breeding stress-resistant melons but also lay a foundation for future research into the potential role of this conserved gene family in integrating stress adaptation with epigenetic regulatory pathways in crops.