Comparative transcriptome analysis by RNA-Seq of the regulation of low temperature responses in Dendranthema morifolium

Cold tolerance is the primary limiting factor affecting the quality and productivity of chrysanthemum (Dendranthema morifolium). However, few studies have investigated the molecular mechanisms underlying the low temperature response in chrysanthemum. In the present study, we used RNA-Seq technology to compare the transcript profiles of chrysanthemum leaves exposed to two different temperatures (20 and −8 °C). A total of 13.54 Gb of clean reads were assembled into 71,971 unigenes with an average length of 694 bp, and 33,282 unigenes were annotated identified from five well-known protein databases. Of these, 9579, 24,252, 7123, 22,554, and 32,891 unigenes were separately identified in the COG, GO, KEGG, Swiss-Prot, and NCBI databases, respectively. Differentially expressed genes (1592 upregulated and 718 downregulated) were identified between the control (CK) and low temperature treatment (T) groups. KEGG pathway enrichment analysis identified 20 significantly different pathways. Many genes encoding important transcription factors (e.g. CBF/DREB, bHLH, MYC, and ZAT) as well as proteins (e.g. CCX, CBP, CML, and MAPK) involved in cold signal transduction were up- or down-regulated in the low temperature treatment group. Genes involved in ABA signal transduction and biosynthesis of unsaturated fatty acids were also identified. The expression profiles of these genes were analyzed during the cold treatment stage. These results provide important information for further studies on gene discovery in chrysanthemum and suggest a potential molecular mechanism for the response to low temperature in this plant species.