Identification and Bioinformatics Analysis of the ClRBOH Gene Family in Cunninghamia lanceolata

To clarify the structural characteristics and expression patterns of the ClRBOH gene family in Chinese fir (Cunninghamia lanceolata), a genome-wide identification and systematic analysis of this gene family were conducted based on the Chinese fir genome. The physicochemical properties, conserved domains, gene structures, chromosomal distribution, cis-acting elements in promoter regions, potential regulatory transcription factors, tissue-specific expression patterns, and phylogenetic relationships of ClRBOH genes were comprehensively analyzed.The results showed that eight ClRBOH gene family members (ClRBOHA–ClRBOHH) were identified in the Chinese fir genome and distributed across five chromosomes. All encoded proteins were predicted to be localized to the plasma membrane and contained the typical NADPH_Ox conserved domain. A total of 27 cis-acting elements were identified in the promoter regions of ClRBOHs, including six core transcription-related elements, four light-responsive elements, seven hormone-responsive elements, and ten stress- and development-related elements. Using a deep learning-based approach, 55 potential regulatory transcription factors were predicted, among which 39 showed significant correlations with ClRBOH gene expression in transcriptome data. Expression pattern analysis revealed that ClRBOHA and ClRBOHF were highly expressed in reproductive-related tissues such as seeds and endosperm; ClRBOHC, ClRBOHD, ClRBOHF, ClRBOHG, and ClRBOHH showed relatively high expression in roots; whereas ClRBOHB exhibited low expression in all examined tissues. Phylogenetic analysis indicated that the plant RBOH gene family could be divided into five major clades. The eight ClRBOH members were distributed in clades II, III, IV, and V, and clustered within the same or closely related subclades as gymnosperm RBOH members, suggesting that the ClRBOH gene family is more closely related to gymnosperms and exhibits distinct gymnosperm lineage characteristics.