Transcriptome profiling of Eucalyptus nitens reveals deeper insight into the molecular mechanism of cold acclimation and deacclimation process

Abstract

Eucalyptus nitens (H. Deane & Maiden) is a fast-growing species used principally for pulpwood and solid-wood production. Due to its cold tolerance, it is preferred over other Eucalyptus species at high elevations. To get a deeper insight in the molecular mechanisms of cold acclimation, the transcriptome profiling by RNA-Seq in plants of E. nitens under cold acclimation and deacclimation process was compared in order to identify differentially expressed genes (DEGs). Transcriptomes from control, cold acclimated to chilling temperature, cold acclimated at freezing temperature, and deacclimation condition were compared using Eucalyptus grandis as reference genome. The differential expression analysis allowed the identification of a total of 1600 DEGs out of which 1088 and 1071 were identified in response to cold acclimation and deacclimation, respectively. The gene ontology analysis revealed that DEGs were significantly enriched in response to stimulus, response to abiotic stimulus, membrane, catalytic activity, and cell periphery. Furthermore, the biochemical pathways analysis revealed a large number of DEGs represented in the biosynthesis of phenylpropanoids, specifically flavonoid biosynthesis likely to support ROS scarvening, genes related to photosynthesis, genes that take part in glycolysis/gluconeogenesis related to starch biosynthesis pathway, and genes represented in carotenoid biosynthesis pathway suggesting a role in the regulation of ABA synthesis, which has been previously involved in stress tolerance. A total of 115 DEGs corresponding to transcription factors were identified, being the most represented families AP2, MYB, and WRKY. Expression of six DEGs was validated using qRT-PCR that further supported the in silico results. The present study provides a comprehensive view of global gene expression and revealed valuable information about the dynamic and complex nature of gene expression occurring during cold acclimation and deacclimation process in E. nitens.