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Castor (Ricinus communis L.) is an important oilseed crop worldwide, and is also considered as one of the most promising plants for alkali-affected soil amelioration in the northeast of China. Seed germination plays a vital role in seedling establishment, and is always sensitive to alkali stress. However, little is known about the dynamic changes and regulatory mechanisms of gene expression and metabolic processes of this species during germination stage under alkali stress. In the present study, physiological, metabolome and transcriptome responses in germinating seeds of castor were investigated when exposed to 0, 50, 100 and 150 mM alkalinity (NaHCO 3). The results showed that alkali stress sharply decreased germination percentage. The Na+ content increased but K+ content decreased under alkalinity. In addition, the malondialdehyde and proline contents increased with the increasing alkalinities. Meanwhile, 50, 100 and 150 mM alkalinity induced 31, 48 and 113 differential metabolites, respectively. Furthermore, transcriptome profiling result showed that there were 138, 845 and 694 differentially expressed genes in the seeds under different concentrations alkali stresses, respectively. The integrating analysis of metabolite and gene expression changes indicating that germination response of castor seeds under alkali stress was closely related to amino acid metabolism, carbohydrate metabolism, lipid metabolism and nucleotide metabolism. The adaptive strategies of castor seeds under alkaline stress were promoting amino acid metabolism and tricarboxylic acid cycle to regulate osmotic balance and ROS level; as well as providing materials and energy for secondary metabolism, although alkali stress affected the membrane fluidity due to the reduction of unsaturated fatty acid content. Moreover, castor seeds increased metabolites on nucleotide biosynthesis to ensure their germination process under alkaline salt stress. The present research provides a deeper insight into overall understanding alkali-tolerant mechanisms of oil crops during germination in a holistic level. • l Using metabolomics and transcriptomics explored physiological adaptation mechanisms of castor seeds under alkali stress. • l 31, 48 and 113 differential metabolites and 138, 845 and 694 differentially expressed genes were found under alkali stress. • l Germination of castor at alkalinity was closely related to amino acid, carbohydrate, lipid and nucleotide metabolisms. • l Seeds of castor promoted amino acid metabolism and tricarboxylic acid cycle under stress. l Seeds of castor provided materials and energy for secondary metabolism under stress. [ABSTRACT FROM AUTHOR]