Identification of heat-responsive genes in carnation (Dianthus caryophyllus L.) by RNA-seq

Abstract

Carnation (Dianthus caryophyllus L.) is an important flower crop, having substantial commercial value as a cut-flower due to the long vase-life and wide array of flower colors and forms. Standard carnation varieties perform well under cool climates but are very susceptible to high temperatures which adversely affect the yield and the quality of the cut-flowers. Despite several studies of carnation contributing to the number of expressed sequence tags (ESTs), transcriptomic information of this species remains very limited, particularly regarding abiotic stress-related genes. Here, transcriptome analysis was performed to generate expression profiles of heat stress (HS)-responsive genes in carnation. We sequenced a cDNA library constructed with mixed RNA from carnation leaves subjected to 42°C HS (0, 0.5, 1, and 2 h) and 46°C HS (0.5, 1, and 2 h), and obtained 45,604,882 high quality paired-end reads. After de novo assembly and quantitative assessment 99,255 contigs were generated with an average length of 1053 bp. We then obtained functional annotations by aligning contigs with public protein databases including NR, SwissProt, KEGG, and COG. Using the above carnation transcriptome as the reference, we compared the effects of high temperature treatments (42°C: duration 0.5, 2, or 12 h) delivered to aseptic carnation seedlings, relative to untreated controls, using the FPKM metric. Overall, 11,471 genes were identified which showed a significant response to one or more of the three HS treatment times. In addition, based on GO and metabolic pathway enrichment analyses, a series of candidate genes involved in thermo-tolerance responses were selected and characterized. This study represents the first expression profiling analysis of D. caryophyllus under heat stress treatments. Numerous genes were found to be induced in response to HS, the study of which may advance our understanding of heat response of carnation.

Transcriptomic Responses of Dove Tree (Davidia involucrata Baill.) to Heat Stress at the Seedling Stage

“…With respect to the molecular function category, "binding" (19,041 unigenes) and "catalytic activity" (14,935 unigenes) were mostly assigned. Consistent with our results, the aforementioned most highly represented GO terms were also observed in transcriptome analyses of other plant species under heat stress [31,32,43]. Those groups of "nucleic acid binding transcription factor activity" (1097 unigenes), "signaling" (2374 unigenes), "transporter activity" (2468 unigenes), and "response to stimulus" (4699 unigenes) have been implicated in plant stress responses, but with lower numbers of assigned unigenes.…”

“…Heat stress is initially perceived by the leaf, which subsequently brings about physiological and biochemical alterations at the whole plant level [50,51]. Moreover, researchers have expended a lot of effort on studying heat response mechanisms in leaf tissues, including analyses of heat-induced leaf transcriptome changes [20,30,32,33,43]. Therefore, healthy mature leaves of approximately the same size were used for the transcriptome analysis of heat stress response in D. involucrata.…”

“…After a one-week adaptation in growth chambers, D. involucrata seedlings were subjected to the 42 • C heat treatment, and leaf tissues were collected at time points 0, 1, 6, and 12 h after the start of heat treatment for transcriptome sequencing. Similarly, time-course gene expression profiling was conducted in carnation (Dianthus caryophyllus L.) leaves in response to the 42 • C heat treatment within 12 h [43].…”

“…In higher plants, heat stress is known to redirect protein synthesis via a reduction in the synthesis of normal proteins concomitantly with a remarkable enhancement in the transcription and translation of Hsps [54]. Mounting evidence suggests that transcript abundance of Hsps along with chaperones is implicated in heat stress adaptation [30][31][32][33]43]. Hsps serve as molecular chaperones that are responsible for the folding, assembly, translocation and degradation of protein molecules, and they play paramount roles in combating stresses through re-establishing normal protein conformation and, thereby, cellular homeostasis [13,44].…”

Dynamic Transcriptome Analysis of Anther Response to Heat Stress during Anthesis in Thermotolerant Rice (Oryza sativa L.)

“…Transcriptomics have been used to study the molecular mechanisms of thermotolerance in wheat [11], tomato [12], potato [13], and carnation [14]; consequently, multiple genes and pathways have been identified as heat-responsive. This information has helped us to understand how plants sense and respond to heat stress.…”