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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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The numbers of DTGs identified in comparisons between pairs of libraries.
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Fig1: The numbers of DTGs identified in comparisons between pairs of libraries.

Mentions: The quality of the RNA-Seq dataset is assessed by gene coverage, which is the percentage of a gene covered by reads. This value is determined as the ratio of the base number in a gene covered by unique mapping reads to the total bases number of that gene. The distribution of the six libraries was presented in Additional file 3: Figure S3. In addition, transcript abundances for each gene (Additional file 4: Table S1) were calculated according to the method following Mortazavi et al. [31]. Moreover, differential transcription was identified through pair-wise comparison between various libraries, by setting a threshold FDR of 0.001 and a│log2 ratio│ of 1 based on the algorithm developed by Audic et al. [32]. From the seven comparisons, including treatment CKA (CK vs A), CKB1 (CK vs B1), CKB2 (CK vs B2), CKC1 (CK vs C1), CKC2 (CK vs C2), AC1(A vs C1), and AC2(A vs C2), the results showed that a large number of DTGs were identified (Additional files 5, 6, 7, 8, 9, 10 and 11: Table S2-8). The number of DTGs detected was as follows: treatment CKA, 3,779 (2,096 up- and 1,683 down-regulated); CKB1, 337 (250 and 87); CKB2, 718 (571 and 147); CKC1, 3,722 (2,271 and 1,451); CKC2, 4,119 (2,611 and 1,508); AC1, 194 (169 and 25); and AC2, 111 (92 and 19) (Figure 1). These results indicated that more DTGs were identified in the treatments, which underwent a prior CA (A, C1 and C2), as compared to the treatments which didn’t undergo CA (B1 and B2). In addition, a smaller number of DTGs was found in A vs C1 and A vs C2 comparisons than in CK vs B1 and CK vs B2. Moreover, on extending the freezing treatment, fewer DTG were detected in A vs C2 comparison than in A vs C1. However, contrary results were obtained in case of CK vs B1 and CK vs B2 comparisons. Based on the assumption that genes with similar expression patterns usually exhibit functional correlation, the consistency of the DTGs was checked by multiple comparisons clustering among the CKA, CKC1 and CKC2; between the CKB1 and CKB2 treatments; and between the comparisons, A vs C1 and A vs C2. A total of 2,340 DTGs were observed in the first multiple comparison clustering, out of which, only three genes behaved inconsistently (that is, showed up-regulation in one treatment and down-regulation in the other, or vice versa). Of the 2,337 consistent DTGs, 1,410 were up- and 927 were down-regulated (Additional file 12: Table S9). In the second multiple comparison clustering, 188 DTGs (142 up- and 46 down-regulated) were obtained (Additional file 13: Table S10), and all were found to be consistent. In the third comparison clustering between A vs C1 and A vs C2, 38 DTGs (37 up- and 1 down-regulated) showed consistency (Additional file 14: Table S11).Figure 1


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)

The numbers of DTGs identified in comparisons between pairs of libraries.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig1: The numbers of DTGs identified in comparisons between pairs of libraries.
Mentions: The quality of the RNA-Seq dataset is assessed by gene coverage, which is the percentage of a gene covered by reads. This value is determined as the ratio of the base number in a gene covered by unique mapping reads to the total bases number of that gene. The distribution of the six libraries was presented in Additional file 3: Figure S3. In addition, transcript abundances for each gene (Additional file 4: Table S1) were calculated according to the method following Mortazavi et al. [31]. Moreover, differential transcription was identified through pair-wise comparison between various libraries, by setting a threshold FDR of 0.001 and a│log2 ratio│ of 1 based on the algorithm developed by Audic et al. [32]. From the seven comparisons, including treatment CKA (CK vs A), CKB1 (CK vs B1), CKB2 (CK vs B2), CKC1 (CK vs C1), CKC2 (CK vs C2), AC1(A vs C1), and AC2(A vs C2), the results showed that a large number of DTGs were identified (Additional files 5, 6, 7, 8, 9, 10 and 11: Table S2-8). The number of DTGs detected was as follows: treatment CKA, 3,779 (2,096 up- and 1,683 down-regulated); CKB1, 337 (250 and 87); CKB2, 718 (571 and 147); CKC1, 3,722 (2,271 and 1,451); CKC2, 4,119 (2,611 and 1,508); AC1, 194 (169 and 25); and AC2, 111 (92 and 19) (Figure 1). These results indicated that more DTGs were identified in the treatments, which underwent a prior CA (A, C1 and C2), as compared to the treatments which didn’t undergo CA (B1 and B2). In addition, a smaller number of DTGs was found in A vs C1 and A vs C2 comparisons than in CK vs B1 and CK vs B2. Moreover, on extending the freezing treatment, fewer DTG were detected in A vs C2 comparison than in A vs C1. However, contrary results were obtained in case of CK vs B1 and CK vs B2 comparisons. Based on the assumption that genes with similar expression patterns usually exhibit functional correlation, the consistency of the DTGs was checked by multiple comparisons clustering among the CKA, CKC1 and CKC2; between the CKB1 and CKB2 treatments; and between the comparisons, A vs C1 and A vs C2. A total of 2,340 DTGs were observed in the first multiple comparison clustering, out of which, only three genes behaved inconsistently (that is, showed up-regulation in one treatment and down-regulation in the other, or vice versa). Of the 2,337 consistent DTGs, 1,410 were up- and 927 were down-regulated (Additional file 12: Table S9). In the second multiple comparison clustering, 188 DTGs (142 up- and 46 down-regulated) were obtained (Additional file 13: Table S10), and all were found to be consistent. In the third comparison clustering between A vs C1 and A vs C2, 38 DTGs (37 up- and 1 down-regulated) showed consistency (Additional file 14: Table S11).Figure 1

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