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Background  Low temperature is a major factor influencing the growth and development of Chinese jujube ( Ziziphus jujuba  Mill.) in cold winter and spring. Little is known about the molecular mechanisms enabling jujube to cope with different freezing stress conditions. To elucidate the freezing-related molecular mechanism, we conducted comparative transcriptome analysis between ‘Dongzao’ (low freezing tolerance cultivar) and ‘Jinsixiaozao’ (high freezing tolerance cultivar) using RNA-Seq.    Results  More than 20,000 genes were detected at chilling (4 °C) and freezing (− 10 °C, − 20 °C, − 30 °C and − 40 °C) stress between the two cultivars. The numbers of differentially expressed genes (DEGs) between the two cultivars were 1831, 2030, 1993, 1845 and 2137 under the five treatments. Functional enrichment analysis suggested that the metabolic pathway, response to stimulus and catalytic activity were significantly enriched under stronger freezing stress. Among the DEGs, nine participated in the Ca 2+  signal pathway, thirty-two were identified to participate in sucrose metabolism, and others were identified to participate in the regulation of ROS, plant hormones and antifreeze proteins. In addition, important transcription factors ( WRKY ,  AP2 / ERF ,  NAC  and  bZIP ) participating in freezing stress were activated under different degrees of freezing stress.    Conclusions  Our research first provides a more comprehensive understanding of DEGs involved in freezing stress at the transcriptome level in two  Z. jujuba  cultivars with different freezing tolerances. These results may help to elucidate the molecular mechanism of freezing tolerance in jujube and also provides new insights and candidate genes for genetically enhancing freezing stress tolerance.

Comparative transcriptome profiling reveals cold stress responsiveness in two contrasting Chinese jujube cultivars