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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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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.
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Fig2: 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.

Mentions: In the treatment CKA, 1,535 of the 3,779 DTGs could be assigned a GO term; the equivalent number for other comparisons were as follows: treatment CKB1, 155/337; CKB2, 246/718; CKC1, 1,522/3722; CKC2, 1,691/4119; A vs C1, 60/194; and A vs C2, 30/111 (Additional file 15: Table S12). For CK vs A, 21 GO classes fell into the categories “biological process”, 12 into “cellular component” and 11 into “molecular function”. The equivalent distribution in CK vs B1 was 18, 10, and 7; in CK vs B2, 20, 11 and 9; in both, CK vs C1 and CK vs C2, 21, 12, and 11; in A vs C1, 17, 9, and 5; and in A vs C2, 11, 7, and 5. The major classes of biological process among the DTGs in CK vs A comparison were “metabolic process”, “cellular process”, “single organism process”, “response to stimulus”, “localization”, “establishment localization”, “biological regulation” and “regulation of biological process”; the predominant cellular components were “cell”, “cell part”, “organelle” and “organelle part”; and for molecular function “binding”, “catalytic activity”, “transporter activity”, “nucleic acid binding transcription factor activity” and “antioxidant activity”. Only a few genes belonged to the categories “cell killing”, “electron carrier activity”, “positive regulation of biological process”, “extracellular matrix”, “receptor activity”, “cell junction”, “protein binding transcription factor activity” and “carbon utilization”. The details of GO classification of DTGs in CK vs A, and other comparisons are presented in Figure 2. Plant hormone signal transduction pathways (mediated by either auxin or gibberellin) were well represented, particularly those associated with auxin-mediated signalling. Low temperature sensing and signalling genes influenced by Ca2+, as well as other protein kinases were also identified. A number of TF families, genes encoding functional proteins and post-translational regulated genes were represented.Figure 2


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)

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.
© Copyright Policy - open-access
Related In: Results  -  Collection

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Fig2: 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.
Mentions: In the treatment CKA, 1,535 of the 3,779 DTGs could be assigned a GO term; the equivalent number for other comparisons were as follows: treatment CKB1, 155/337; CKB2, 246/718; CKC1, 1,522/3722; CKC2, 1,691/4119; A vs C1, 60/194; and A vs C2, 30/111 (Additional file 15: Table S12). For CK vs A, 21 GO classes fell into the categories “biological process”, 12 into “cellular component” and 11 into “molecular function”. The equivalent distribution in CK vs B1 was 18, 10, and 7; in CK vs B2, 20, 11 and 9; in both, CK vs C1 and CK vs C2, 21, 12, and 11; in A vs C1, 17, 9, and 5; and in A vs C2, 11, 7, and 5. The major classes of biological process among the DTGs in CK vs A comparison were “metabolic process”, “cellular process”, “single organism process”, “response to stimulus”, “localization”, “establishment localization”, “biological regulation” and “regulation of biological process”; the predominant cellular components were “cell”, “cell part”, “organelle” and “organelle part”; and for molecular function “binding”, “catalytic activity”, “transporter activity”, “nucleic acid binding transcription factor activity” and “antioxidant activity”. Only a few genes belonged to the categories “cell killing”, “electron carrier activity”, “positive regulation of biological process”, “extracellular matrix”, “receptor activity”, “cell junction”, “protein binding transcription factor activity” and “carbon utilization”. The details of GO classification of DTGs in CK vs A, and other comparisons are presented in Figure 2. Plant hormone signal transduction pathways (mediated by either auxin or gibberellin) were well represented, particularly those associated with auxin-mediated signalling. Low temperature sensing and signalling genes influenced by Ca2+, as well as other protein kinases were also identified. A number of TF families, genes encoding functional proteins and post-translational regulated genes were represented.Figure 2

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