Genome-Wide Identification of the U-Box Gene Family and Expression Analysis in Response to Salt Stress in Melon

The U-box proteins (PUBs), as a prominent family of E3 ubiquitin ligases, have been reported to participate in diverse physiological processes, such as plant development, growth regulation, and adaptation to abiotic and biotic stresses. Nevertheless, a comprehensive genome-wide survey and functional investigation of the U-box family in melon remain limited. In this study, a total of 50 CmPUB genes harboring the U-box domain were identified and distributed across the 12 melon chromosomes. Phylogenetic analysis among melon, cucumber, tomato and Arabidopsis divided the 50 CmPUBs into six subfamilies. CmPUB37/48/49 are orthologous to salt stress-responsive AtPUB18/19 in Arabidopsis. Intraspecies collinearity analyses detected 11 homologous gene pairs within the CmPUB family and 15 to 67 collinear genes among five other species, respectively, based on the interspecies collinearity analyses. Promoter analysis revealed that CmPUBs had diverse and abundant cis-acting regulatory elements involved in light signal transduction, phytohormone regulation, and stress responses, as well as plant development. Transcriptome analysis of the CmPUBs in melon under salt stress revealed that most CmPUBs exhibited temporally differentiated expression patterns, with some genes being rapidly induced at the early stage of stress and continuously upregulated at the late stage. Physiological measurements under salt stress indicated that leaves were the primary tissue responding to salt-induced oxidative damage, and that the salt-tolerant line M4-116 alleviated this damage by maintaining higher superoxide dismutase (SOD) and catalase (CAT) activities and lower malondialdehyde (MDA) accumulation than the salt-sensitive line M4-75. Quantitative real-time PCR (qRT-PCR) was conducted using leaf tissues harvested at multiple time intervals. The expression patterns were compared between salt-tolerant and salt-sensitive cultivars, revealing that transcript levels were markedly elevated in the salt-tolerant cultivar under salt stress conditions. In conclusion, this study provides a foundation for further functional studies of U-box genes and offers new insights into stress responses in melon.