The study focuses on the Cyclic nucleotide-gated ion channels (CNGCs) proteins in citrus, aiming to investigate their potential roles. A total of 33 CcCNGC proteins were identified and characterized in Citrus clementina using a genome-wide method. The study revealed that these proteins share a conserved CNGC domain structurally but exhibit significant differences in their primary sequence and motif composition. Phylogenetic analysis classified the CcCNGC proteins into 13 subgroups. The cis-elements present in all CcCNGCs promoters were identified and classified, and the number of elements was determined. The results suggested that these genes play important roles in citrus growth and development, as well as in response to biotic and abiotic stresses. Gene expression analysis further supported these findings, demonstrating that CNGC genes were responsive to various plant hormones and Phytophthora nicotianae infection, which causes citrus foot rot. Overall, the study indicated that members of the CcCNGC gene family exhibit structural and functional diversity. Further research is needed to validate the specific functions of individual family members and their roles in citrus physiology and response to stress conditions.

The Dof transcription factor family plays crucial roles in plant growth and stress responses. In this study, we identified 24 Dof genes (CcDof1–CcDof24) from the genome of Citrus clementina (Hort. ex Tan.). Phylogenetic analysis classified these proteins into six distinct clades, revealing evolutionary conservation with Dof members from Arabidopsis and tomato. Analysis of gene structure and conserved motifs showed that most CcDof genes are intronless or contain only a few introns, and their motif compositions are largely consistent with their phylogenetic relationships. Promoter analysis revealed a variety of cis-regulatory elements associated with light responsiveness, hormone signaling, and abiotic/biotic stress responses. Expression profiling demonstrated that CcDof genes exhibit tissue-specific expression patterns and are differentially regulated by various phytohormones (including ABA, SA, GA, and MeJA), low temperature stress, and infection by Phytophthora parasitica. Notably, transient overexpression of CcDof4 and CcDof6 in citrus leaves significantly enhanced resistance to P. parasitica, accompanied by upregulation of SA pathway markers NPR1 and PR1. Our findings provide a systematic characterization of the CcDof family and highlight the important roles of CcDof4 and CcDof6 in mediating citrus disease resistance, likely through modulation of the SA signaling pathway.