Genome-Wide In Silico Identification, Classification, and Evolutionary Analysis of Putative Abiotic Stress-Related CCCH Genes in Carrot

CCCH proteins, a key zinc finger family in plants, are characterized by three cysteine and one histidine residue. They play crucial roles in plant growth, development, and stress responses. Despite their importance, the CCCH gene family has not been previously identified or analyzed in the carrot (Daucus carota) genome. This study identified 71 CCCH-type proteins in carrot. Motif analysis revealed high similarity to CCCH motifs in other plant species, and phylogenetic analysis grouped them into 13 clusters, with Group IV belonging to the RR-TZF class, critical for stress response. Orthologous genes clustered in the same phylogenetic branches, indicating a shared ancestral origin between dicots and monocots. Ka/Ks analysis showed 11 duplicated gene pairs underwent purifying selection, with six pairs showing strong selection. Promoter analysis identified abundant stress-related cis-regulatory elements, such as MYB, MYC, LTR, and ABRE, particularly in Group IV genes. RNA-seq data highlighted tissue-specific expression profiles of CCCH genes under stress and normal conditions. miRNA target analysis revealed 493 binding sites, with associations to 245 Arabidopsis miRNAs. Additionally, the protein interaction network suggested these genes play diverse roles based on their molecular and biological functions. These findings provide a foundation for identifying stress-responsive CCCH transcription factors, paving the way for future studies to enhance carrot stress tolerance.