Identification of the NAC Gene Family in Cuphea hookeriana and Analysis of Its Expression in Response to Cold Stress

This study aimed to investigate the characteristics of the NAC transcription factor family in Cuphea hookeriana and its regulatory mechanisms in response to cold stress, as well as to identify key cold-tolerance genes. Based on whole-genome data, NAC gene family members were systematically identified, and their physicochemical properties, phylogenetic relationships, gene structures, conserved motifs, chromosomal distribution, and syntenic relationships were analyzed. The expression dynamics of ChNAC genes at different time points under cold stress were examined using transcriptome sequencing and qRT-PCR. A total of 218 ChNAC genes were identified, unevenly distributed across 16 chromosomes. Phylogenetic analysis showed that they could be divided into 16 subfamilies, with the NAC2 subfamily containing the most members. Synteny analysis revealed 2,129 duplicated gene pairs and six tandem duplication events, and the Ks distribution curve exhibited two significant peaks at 0.03 and 0.63. Promoter analysis indicated that ChNAC genes are enriched in cis-acting elements such as abscisic acid-responsive (ABRE) elements. Expression analysis under cold stress showed that 18 ChNAC genes were significantly upregulated at 12 h of stress, among which five genes—ChNAC1, ChNAC24, ChNAC130, ChNAC215 and ChNAC217—were validated by qRT-PCR, showing expression trends consistent with the transcriptomic data. In conclusion, the ChNAC gene family in C. hookeriana has undergone multiple duplication events during evolution, and several members are significantly induced by cold stress. Among them, these five genes may serve as core regulatory factors in the cold stress response, providing an important basis for elucidating the molecular mechanisms of cold tolerance in C. hookeriana.