Norway spruce deploys tissue specific canonical responses to acclimate to the 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 Picea abies (L.) H. Karst (Norway spruce), we performed RNA-Sequencing analysis of needles and roots subjected to a chilling progression (5 {degrees}C) followed by 10 days at freezing temperature (-5 {degrees}C). Comparing gene expression responses of needles against Arabidopsis thaliana 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 APETALA 2/ethylene-responsive 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 bHLH101 homolog and other members of the same family with a pervasive role in cold regulation, such as homologs of ICE1 and AKS3 and also homologs of the NAC (anac47 and anac28) and AP2/ERF superfamilies (DREB2 and ERF3), providing new functional insights into cold stress response strategies in Norway spruce. One sentence summaryNorway spruce shares elements of the cold regulon described in herbaceous species but has undescribed components that contribute to the cold tolerance of this evergreen coniferous species.