Norway spruce deploys tissue specific canonical responses to acclimate to cold

Cold acclimation in plants is a complex phenomenon involving numerous stress-responsive transcriptional and metabolic pathways. Existing gene expression studies have primarily addressed short-term cold acclimation responses in herbaceous plants, while few have focused on perennial evergreens, such as conifers, that survive extremely low temperatures during winter. To characterize the transcriptome changes during cold acclimation in (L.) H. Karst (Norway spruce), we performed RNA-Sequencing analysis of needles and roots subjected to a chilling progression (5 °C) followed by 10 days at freezing temperature (−5 °C). Comparing gene expression responses of needles against L. (Arabidopsis) leaves, our results showed that early transient inductions were observed in both species but the transcriptional response of Norway spruce was delayed. Our results indicate that, similar to herbaceous species, Norway spruce principally utilizes early response transcription factors (TFs) that belong to the ETALA /thylene-esponsive element binding factor (AP2/ERF) superfamily and NACs. However, unique to the Norway spruce response was a large group of TFs that mounted a late transcriptional response to low temperature. A predicted regulatory network analysis identified key conserved TFs, including a root-specific homolog and other members of the same family with a pervasive role in cold regulation, such as homologs of and and also homologs of the NAC ( and ) and AP2/ERF superfamilies ( and ), providing new functional insights into cold stress response strategies in Norway spruce.