De novo transcriptome sequencing and gene expression profiling of Pinus sibirica under different cold stresses

Abstract Background: Pinus sibirica is an evergreen conifer tree species with strong cold stress. However, the transcriptional regulation patterns in response to cold stress have not been reported for P. Sibirica. To gain deeper insights into its regulation process of cold tolerance, transcriptome profiling analyses and 12 physiological indices measurement were performed under cold stress (-20 ℃) over time. Results: More than 54.1 million clean reads were produced, which were assembled into 97,376 unigenes. Among them, 56,994 unigenes had homology with known genes, 36,836 were assigned to 51 GO (gene ontology) categories and 46,972 were assigned to 24 COG (clusters of orthologous group) categories. P. sibirica showed the highest similarity with sequences from Picea sitchensis. In total, 871, 1397 and 872 DEGs (differentially expressed genes) were identified upon exposure to cold for 6 h, 24 h and 48 h at -20 ℃, respectively. Nine physiological indices increased significantly (P<0.05) under cold stress, including membrane permeability, relative conductivity, reactive oxygen species, malonaldehyde, peroxidase activity, catalase activity, soluble sugar, soluble protein and proline content. With extension of the cold stress time, 9 physiological indices generally showed a trend toward first an increase and then a decrease. The net photosynthetic rate, stomatal conductance and transpiration rate in P. sibirica dropped sharply (P<0.05) in response to cold stress, and they were also decreased significantly (P<0.05) with extension of the stress time at -20 ℃.Conclusions: There were two cold signal transduction pathways in P. sibirica, the Ca2+ and ABA (abscisic acid) pathways. The AP2 (ethylene-responsive transcription factor) family and some other transcription factors played an important role in transcriptional regulation. P. sibirica underwent antioxidant and osmotic regulation with changes in the expression of genes related to cold resistance. Photosynthesis was inhibited, and more DEGs associated with photosynthesis were downregulated under cold stress. The DEGs identified in cold signal sensing and transduction and transcriptional, antioxidant and osmotic regulation can provide genetic resources for the improvement of cold-tolerant characters in other conifer tree species and facilitate understanding of molecular control mechanism related to cold responses.