Genome-wide identification and expression profile of CYP genes in rubber tree (Hevea brasiliensis)

Introduction: Cytochrome P450 monooxygenases (CYPs) are crucial in plant secondary metabolism, catalyzing diverse biochemical reactions, defense, and stress adaptation. Hevea brasiliensis is the primary source of natural rubber, but its CYP family remains underexplored, which may play essential roles in rubber biosynthesis and environmental tolerance. Method and Result: n this study, we systematically identified 238 HbCYP genes in H. brasiliensis, classified them into 9 clans and 43 subfamilies, with Clan 71 contraction and Clan 72 and Clan 85 emerging as the most expansive clans. Gene structure analysis revealed that 68.87% of A-type HbCYPs have one intron. Separately, analysis of conserved motifs in promoter regions identified a high abundance of cis-acting elements, including 456 related to methyl jasmonate (meJA) responsiveness and 3,302 related to light responsiveness. Genome evolution analysis indicated that 64 tandem and 119 WGD or segmental duplications significantly contributed to the expansion of the HbCYP family, also supported by orthologous genes with other four species. Tissue-specific profiling revealed differential HbCYPs expression across H. brasiliensis organs. Notably, meJA and ethylene (ET) treatments differentially expressed 93 and 60 HbCYP genes, respectively. Gene Ontology (GO) analysis and real-time quantitative polymerase chain reaction (RT-qPCR) validation of these genes revealed their significant contribution in rubber biosynthetic pathways. Protein interaction networks highlighted collaborations between HbCYPs and key rubber biosynthesis enzymes, including 3-hydroxy-3-methylglutaryl-CoA synthase (HMGS), and these results demonstrate functional diversification within the HbCYP family associated with rubber biosynthesis. Conclusion: Collectively, this study provides the first comprehensive genome-wide analysis of the HbCYP family in H. brasiliensis, offering insights into their evolutionary dynamics and functional diversification. The results establish a foundation for future research on CYP-mediated rubber biosynthesis and stress adaptation, with implications for molecular breeding of high-yield and stress-tolerant rubber tree cultivars.