Genome-Wide Identification and Expression Analysis of the TRM Gene Family in Melon (Cucumis melo L.)

Melon (Cucumis melo L.), a widely cultivated species of the Cucurbitaceae family, is one of the most economically important fruit crops globally. TRM proteins have been implicated in the regulation of plant development, including processes related to cell division, cell expansion, and organ morphology. Although the functions of TRM family members have been extensively characterized in Arabidopsis, tomato, and cucumber, their roles in melon fruit development remain poorly understood. In this study, a total of 22 CmTRM (Cucumis melo) genes containing the conserved DUF3741 and DUF4378 domains were identified from the melon genome data via bioinformatics approaches. Subsequently, we systematically analyzed the physicochemical properties of CmTRM-encoded proteins as well as the chromosomal distribution, gene organization, conserved motif patterns, and promoter regulatory elements of all 22 CmTRM members. Notably, the high-accuracy three-dimensional structure prediction of the CmTRM proteins were predicted using the AlphaFold3, intraspecific collinearity analyses of the CmTRMs were performed, seven pairs of collinear genes were identified. Additionally, phylogenetic analysis revealed that the CmTRM proteins could be classified into eight distinct clades, with CmTRM05 and CmTRM21 assigned to Group I. We performed quantitative real-time PCR (qRT-PCR) analysis on all 22 CmTRMs. The results showed that CmTRM05, CmTRM19 and CmTRM21 exhibited significantly distinct stage-specific expression patterns across fruit developmental gradients between the two melon accessions with contrasting fruit phenotypes. These three genes were therefore prioritized as candidate genes for subsequent genetic functional validation. Furthermore, subcellular localization assays revealed that CmTRM05 primarily resides in the cytoplasm. In conclusion, this study advances our understanding of the TRM gene family in melon and offers a theoretical and practical basis for investigating the influence of TRM on melon fruit shape, which is of great significance for developing new melon varieties with desirable fruit shapes.