Genome-wide characterization of the cytochrome P450 superfamily reveals candidate genes associated with specialized metabolism and abiotic stress responses in Dendrobium nobile

Abstract Background Plants produce a diverse range of bioactive molecules, including hormones, specialized metabolites, and defense-related compounds. Cytochrome P450 (CYP) proteins contribute substantially to this chemical diversity. This study systematically identified 242 CYP family genes in Dendrobium nobile L. and analyzed their phylogenetic relationships, protein motifs, gene structures, chromosomal locations, collinearity, cis-elements in the promoter, and expression patterns under abiotic stress and in different tissues. Results The 242 DnCYP proteins were classified into 39 families across nine clans. Tandem duplication events were observed in several CYP family genes, particularly in the CYP71, CYP72, CYP76, CYP81, CYP92, and CYP704 families. Among the species examined, CYP71K subfamily genes were detected only in orchids and were more numerous in D. nobile than in the other Dendrobium species analyzed. The tissue transcript profiles of five genes ( DnCYP71K30 , DnCYP71K32 , DnCYP71K33 , DnCYP71K34 , and DnCYP71B1 ) located on chromosome 15 were positively correlated with those of upstream pathway genes associated with picrotoxane-type sesquiterpene alkaloid (PSA) biosynthesis such as DnHMGR and DnTPSs . In addition, RNA-seq analysis identified a subset of genes with altered transcript abundance under MeJA, drought, and temperature treatments; putative stress-responsive cis-elements were also detected in their promoters. qRT-PCR reproduced the direction of expression change for selected genes. Conclusions These results provide a resource for prioritizing DnCYP candidates, whose biochemical and physiological functions require direct experimental validation.