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Background  Low temperature restricts the planting range of all crops, but cold acclimation induces adaption to cold stress in many plants.  Camellia sinensis , a perennial evergreen tree that is the source of tea, is mainly grown in warm areas.  Camellia sinensis var. sinensis  (CSS) has greater cold tolerance than  Camellia sinensis var. assamica  (CSA). To gain deep insight into the molecular mechanisms underlying cold adaptation, we investigated the physiological responses and transcriptome profiles by RNA-Seq in two tea varieties, cold resistant SCZ (classified as CSS) and cold susceptible YH9 (classified as CSA), during cold acclimation.    Results  Under freezing stress, lower relative electrical conductivity and higher chlorophyll fluorescence (Fv/Fm) values were detected in SCZ than in YH9 when subjected to freezing acclimation. During cold treatment, 6072 and 7749 DEGs were observed for SCZ and YH9, respectively. A total of 978 DEGs were common for both SCZ and YH9 during the entire cold acclimation process. DEGs were enriched in pathways of photosynthesis, hormone signal transduction, and transcriptional regulation of plant-pathogen interactions. Further analyses indicated that decreased expression of  Lhca2  and higher expression of  SnRK2.8  are correlated with cold tolerance in SCZ.    Conclusions  Compared with CSA, CSS was significantly more resistant to freezing after cold acclimation, and this increased resistance was associated with an earlier expression of cold-induced genes. Because the greater transcriptional differentiation during cold acclimation in SCZ may contribute to its greater cold tolerance, our studies identify specific genes involved in photoinhibition, ABA signal conduction, and plant immunity that should be studied for understanding the processes involved in cold tolerance. Marker-assisted breeding focused on the allelic variation at these loci provides an avenue for the possible generation of CSA cultivars that have CSS-level cold tolerance.    Electronic supplementary material  The online version of this article (10.1186/s12864-019-5988-3) contains supplementary material, which is available to authorized users.

Comparative transcriptomic analysis reveals gene expression associated with cold adaptation in the tea plant Camellia sinensis