Genome-wide identification, characterization, and expression profile analysis of the caffeic acid O-methyltransferases gene family in sweet orange (Citrus sinensis L.) in response to Penicillium digitatum infection

Caffeic acid O-methyltransferases (COMTs), key methylating enzymes in the phenylpropanoid pathway, play a vital role in plant defense against various environmental stresses. To date, numerous plant COMT gene families have been studied. Sweet orange (Citrus sinensis L.), the primary cultivated variety of orange, accounts for more than 80% of global orange production. However, high-incidence infection by Penicillium digitatum inflicts substantial economic losses on the sweet orange industry. COMTs constitute a known major disease resistance gene family potentially involved in related responses. Nevertheless, comprehensive research on the COMT gene family in sweet orange is lacking. This study identified the COMT gene from the sweet orange genome (v3.0) and conducted a comprehensive analysis of this gene family, including phylogenetic analysis, gene structure, promoter cis-acting elements, and chromosomal localization. Using experimental data from our research group, we analyzed the expression pattern of the COMT gene in sweet orange fruits infected with P. digitatum. This study identified 39 COMTs genes from the sweet orange genome (v3.0), which were classified into five subfamilies based on phylogeny and gene structure. The promoter regions contain abundant cis-acting elements responsive to plant hormones and stress. The genes are unevenly distributed across nine chromosomes, with the highest number located on chromosome 5. 13 CsCOMTs genes were enriched in the phenylpropanoid biosynthesis pathway. 29 CsCOMTs genes showed potential targeting relationships with 68 sweet orange miRNAs. 14 CsCOMTs genes were expressed during P. digitatum infection, with significant expression differences observed in genes such as CsCOMT23, CsCOMT25, and CsCOMT26. This indicates the CsCOMT gene family plays a crucial role in sweet orange defense against P. digitatum. This study provides the first comprehensive framework of the sweet orange CsCOMT gene family, revealing that genes such as CsCOMT23, CsCOMT25, and CsCOMT26 participate in the sweet orange response to P. digitatum infection. These findings lay the foundation for further investigations into the biological functions of sweet orange CsCOMTs in response to biotic stress.