Genome-wide characterization of the melon (Cucumis melo L.) FtsH-related protein family and expression analysis of CmFtsH10 during fruit development

FtsH (Filamentous temperature-sensitive H) metalloproteases are critical for membrane protein quality control and chloroplast homeostasis. However, the composition, evolution, and expression patterns of the FtsH-related protein family in melon ( Cucumis melo L.) remain largely uncharacterized. Here, we identified 12 melon FtsH-related proteins (CmFtsHs), comprising seven typical FtsH proteases and five FtsHi pseudo-proteases. Phylogenetic analysis assigned these proteins to six of the seven known groups. Synteny analysis revealed that CmFtsH3/CmFtsH10 is the only segmentally duplicated gene pair, with a Ka/Ks ratio of 0.1041, indicating strong purifying selection. Comparative synteny further showed conserved CmFtsH-containing genomic regions between melon and cucumber, and between melon and watermelon. Promoter analysis identified numerous light- and phytohormone-responsive cis-elements. Most CmFtsHs were highly expressed in leaves, while CmFtsH3, CmFtsHi3, CmFtsH4, and CmFtsH10 also showed elevated expression in flowers. During fruit development, CmFtsHs displayed distinct temporal expression patterns; CmFtsH10 transcript levels peaked at 15 days after pollination, remained relatively high at 20 days after pollination, and subsequently declined. Short-term hormone treatments (ABA, IAA, MeJA, and ethephon) induced hormone- and concentration-specific responses, with CmFtsH10 responding to all four hormones at 2 h. Confocal imaging showed substantial spatial correspondence between the CmFtsH10-EGFP signal and chlorophyll autofluorescence, supporting a predominant association of CmFtsH10 with chloroplasts. Localized visual color differences were observed at some time points following infiltration of ‘Micro-Tom’ tomato fruits with the 35S::CmFtsH10-EGFP construct. Collectively, this study provides a systematic framework for understanding the melon FtsH-related protein family and highlights CmFtsH10 as a candidate for further functional studies in fruit development.