A transcriptomic analysis of Chrysanthemum nankingense provides insights into the basis of low temperature tolerance

Abstract

Background: A major constraint affecting the quality and productivity of chrysanthemum is the unusual period of low temperature occurring during early spring, late autumn, and winter. Yet, there has been no systematic investigation on the genes underlying the response to low temperature in chrysanthemum. Herein, we used RNA-Seq platform to characterize the transcriptomic response to low temperature by comparing different transcriptome of Chrysanthemum nankingense plants and subjecting them to a period of sub-zero temperature, with or without a prior low temperature acclimation.

Results: Six separate RNA-Seq libraries were generated from the RNA samples of leaves and stems from six different temperature treatments, including one cold acclimation (CA), two freezing treatments without prior CA, two freezing treatments with prior CA and the control. At least seven million clean reads were obtained from each library. Over 77% of the reads could be mapped to sets of C. nankingense unigenes established previously. The differentially transcribed genes (DTGs) were identified as low temperature sensing and signalling genes, transcription factors, functional proteins associated with the abiotic response, and low temperature-responsive genes involved in post-transcriptional regulation. The differential transcription of 15 DTGs was validated using quantitative RT-PCR.

Conclusions: The large number of DTGs identified in this study, confirmed the complexity of the regulatory machinery involved in the processes of low temperature acclimation and low temperature/freezing tolerance.

Figure 1

The numbers of DTGs identified in comparisons between pairs of libraries.

Figure 2

Gene Ontology (GO) classification of the DTGs identified in each comparison between a pair of libraries. DTGs were annotated in three categories: biological process, cellular component and molecular function. Y-axis (right) represents the number of DTGs in each category; Y-axis (left) represents the percentage of a specific category of DTGs within that main category. Panels a, b, c, d, e, f and g (left) represents DTGs in the comparison between library CK (22°C) and A (4°C for one week) (CK-VS-A) (right) , library CK and B1 (-5°C for 1 h) (CK-VS-B1) (right), library CK and B2 (-5°C for 2 h) (CK-VS-B2) (right), library CK and C1 (4°C for one week, followed by -5°C for 1 h) (CK-VS-C1) (right), library CK and C2 (4°C for one week, followed by -5°C for 2 h) (CK-VS-C2) (right), library A and C1 (A-VS-C1) (right), and library A and C2 (A-VS-C2) (right) respectively.

Figure 3

qPCR validation for 15 DTGs identified by RNA-Seq in the comparison between CK and A.