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

Ren L, Sun J, Chen S, Gao J, Dong B, Liu Y, Xia X, Wang Y, Liao Y, Teng N, Fang W, Guan Z, Chen F, Jiang J - BMC Genomics (2014)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China. chenfd@njau.edu.cn.

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.

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qPCR validation for 15 DTGs identified by RNA-Seq in the comparison between CK and A.
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Fig3: qPCR validation for 15 DTGs identified by RNA-Seq in the comparison between CK and A.

Mentions: To further verify the expression profiles of genes in our Illumina RNA-Seq results, we have performed a selection of 15 DTGs for their key roles in response to low temperature by qRT-PCR, these incorporated genes encoding serine/threonine-protein kinase, LEA protein, dehydrin, a gibberellin-regulated protein, a jasmonate ZIM-domain protein, and a DEAD-box ATP-dependent RH, along with a selection of TFs (WRKY, DREB, AP2, bHLH and DOF). The qPCR outcomes in each case correlated closely with the transcript abundances estimated from the RNA-Seq output (FigureĀ 3).Figure 3


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

Ren L, Sun J, Chen S, Gao J, Dong B, Liu Y, Xia X, Wang Y, Liao Y, Teng N, Fang W, Guan Z, Chen F, Jiang J - BMC Genomics (2014)

qPCR validation for 15 DTGs identified by RNA-Seq in the comparison between CK and A.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4197275&req=5

Fig3: qPCR validation for 15 DTGs identified by RNA-Seq in the comparison between CK and A.
Mentions: To further verify the expression profiles of genes in our Illumina RNA-Seq results, we have performed a selection of 15 DTGs for their key roles in response to low temperature by qRT-PCR, these incorporated genes encoding serine/threonine-protein kinase, LEA protein, dehydrin, a gibberellin-regulated protein, a jasmonate ZIM-domain protein, and a DEAD-box ATP-dependent RH, along with a selection of TFs (WRKY, DREB, AP2, bHLH and DOF). The qPCR outcomes in each case correlated closely with the transcript abundances estimated from the RNA-Seq output (FigureĀ 3).Figure 3

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China. chenfd@njau.edu.cn.

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.

Show MeSH
Related in: MedlinePlus