Comprehensive Omics Analysis Reveals Cold-Induced Metabolic Reprogramming and Alternative Splicing in .

is an economically important orchid species that is sensitive to cold stress. Understanding the molecular and metabolic mechanisms underlying its response to cold is crucial for developing strategies to improve its cold tolerance. In this study, we constructed a comprehensive cold stress response dataset for and characterized its regulatory landscape in response to varying cold stress conditions. The glycine metabolism-related genes and play pivotal roles in both cold and drought stress adaptation, and their expression is not upregulated by hormones or fungi infection. Carbohydrate metabolism showed specific dynamic changes in freezing injury cells, which involved a variety of hormonal responses. The abundance of sphingolipids was notably higher in the freezing treatment (FT) compared to the freezing recovery (FR) plants, indicating specialized metabolic adaptations at different cold intensities. An alternative splicing (AS) analysis identified 368 DAS genes, with spliceosome pathways significantly enriched. Three key ubiquitination proteins (PKU64802, XP_020672210, and PKU75555) were found to regulate splicing factors, which showed increased abundance in cold stress. This study highlights the roles of metabolic reprogramming and RNA splicing in cold adaptation, revealing a complex molecular network activated in response to cold stress.