Genome-Wide Identification, Characterization, and Expression Analysis of Cyclic Nucleotide-Gated Channel (CNGC) Gene Family in Daucus carota Under Drought Stress and Arbuscular Mycorrhizal Symbiosis

Background Cyclic nucleotide-gated channels (CNGCs) are non-selective cation channels that are involved in key processes in plant signal transduction, ion homeostasis and stress adaptation. Although the CNGC gene family has well-characterized roles in model plants like Arabidopsis thaliana , the roles of these genes in carrot ( Daucus carota ), a highly valuable root crop, have not been well studied. Results A global genome-wide overview revealed 24 DcCNGC genes that are spread out on all eight D. carota chromosomes. These genes were clustered into six groups (I-VI) with phylogenetic analysis which showed conserved orthologous relationships with AtCNGC members and evidence of duplication events. Physicochemical profiling revealed that DcCNGC proteins have a size between 610–2027 amino acids (70.0-226.3 kDa), most of them with a basic isoelectric point (pI 7.17–9.66). The structural analysis showed the presence of conserved domains of cyclic nucleotide-binding (cNMP_binding), ion transport (Ion_trans), and CAP effector domains. The promoter analysis revealed various cis-regulatory factors in response to drought, abscisic acid, jasmonate, salicylate, and light. Ka/Ks ratio analysis revealed that all paralogous pairs of DcCNGC genes diverged under purifying selection (Ka/Ks < 1) that represents a high functional constraint. The AlphaFold3 protein structure prediction showed three-dimensional structure and was used to predict the protein structure of DcCNGC members, which revealed the presence of conserved transmembrane topology and cyclic nucleotide-binding pocket architecture. GO and KEGG enrichment analyses verified functional relevance in ion transport, voltage-gated channel activity, plant-pathogen interaction pathways.The expression analysis of the RNA-seq of drought stress and arbuscular mycorrhizal (AM) symbiosis identified differential expression of several DcCNGC genes, as DcCNGC2a , DcCNGC5 , and DcCNGC8 were upregulated during drought and AM inoculation. Conclusions This research presents the first systematic characterization of the CNGC family of genes in D. carota and a baseline resource to study calcium-mediated responses to abiotic stress. The identified candidate genes, especially, those with drought- and AM-responsive expression patterns, are promising targets in genetic enhancement of carrot under the conditions of water scarcity.