Transcriptome and metabolome analysis of Cycas bifida response to low-temperature stress

Abstract Background Cycas bifida is an endemic species distributed in limited areas of Yunnan and Guangxi, with a notably small population size. Under the context of global climate warming, this species may require introduction to colder habitats. Previous studies have confirmed its weak cold tolerance. To thoroughly investigate the molecular and metabolic mechanisms underlying its response to low temperature, this study employed low-temperature stress treatments combined with transcriptome sequencing and metabolomics technologies for systematic comparative analysis. Results Through multi-omics analysis, this study identified 1,960 differentially expressed genes in Cycas bifida under cold stress, showing an overall upregulation trend. Pathway enrichment analysis confirmed galactose metabolism and flavonoid biosynthesis as key pathways responding to cold stress. Co-expression network analysis revealed significant associations between the MEyellow module and melibiose, and between the MEgreen module and luteolin. Additionally, the core turquoise module was found to mediate a “metabolic trade-off” mechanism through the key gene pair CYCAS_003438/CYCAS_003468, promoting osmoprotectant production via galactose metabolism while suppressing flavonoid synthesis. These results systematically elucidate the molecular mechanisms by which Cycas bifida coordinates multiple gene modules to regulate metabolic pathways in response to cold stress. Conclusion This study identified a key gene module in Cycas bifida that coordinates carbon allocation through a metabolic trade-off mechanism, promoting osmoprotectant synthesis while suppressing flavonoid accumulation. This finding first reveals the suppression of flavonoid metabolism in cycads under cold stress, elucidating a novel mechanism of resource optimization through gene module reprogramming in plants, which provides a theoretical foundation for cold-tolerant breeding.