Highlights • Approximately 120,000 genes were detected in Dn1 during the overwintering stage (the lowest sampling temperature was -25 °C), of which 31,000 genes were differentially expressed. • A total of 1230 differentially expressed genes involved in cold signal perception and transduction were detected in Dn1 during the overwintering stage. • A total of 1715 differentially expressed genes involved in carbohydrate metabolism were detected in Dn1 during the overwintering stage, most of which were enriched in glycolysis/gluconeogenesis and starch and sucrose metabolism.