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Comparative Study
. 2012 Nov 21:12:222.
doi: 10.1186/1471-2229-12-222.

Deep-sequencing transcriptome analysis of chilling tolerance mechanisms of a subnival alpine plant, Chorispora bungeana

Zhiguang Zhao  1 , Lingling Tan, Chunyan Dang, Hua Zhang, Qingbai Wu, Lizhe An
Affiliations
Comparative Study

Deep-sequencing transcriptome analysis of chilling tolerance mechanisms of a subnival alpine plant, Chorispora bungeana

Zhiguang Zhao et al. BMC Plant Biol. .

Abstract

Background: The plant tolerance mechanisms to low temperature have been studied extensively in the model plant Arabidopsis at the transcriptional level. However, few studies were carried out in plants with strong inherited cold tolerance. Chorispora bungeana is a subnival alpine plant possessing strong cold tolerance mechanisms. To get a deeper insight into its cold tolerance mechanisms, the transcriptome profiles of chilling-treated C. bungeana seedlings were analyzed by Illumina deep-sequencing and compared with Arabidopsis.

Results: Two cDNA libraries constructed from mRNAs of control and chilling-treated seedlings were sequenced by Illumina technology. A total of 54,870 unigenes were obtained by de novo assembly, and 3,484 chilling up-regulated and 4,571 down-regulated unigenes were identified. The expressions of 18 out of top 20 up-regulated unigenes were confirmed by qPCR analysis. Functional network analysis of the up-regulated genes revealed some common biological processes, including cold responses, and molecular functions in C. bungeana and Arabidopsis responding to chilling. Karrikins were found as new plant growth regulators involved in chilling responses of C. bungeana and Arabidopsis. However, genes involved in cold acclimation were enriched in chilling up-regulated genes in Arabidopsis but not in C. bungeana. In addition, although transcription activations were stimulated in both C. bungeana and Arabidopsis, no CBF putative ortholog was up-regulated in C. bungeana while CBF2 and CBF3 were chilling up-regulated in Arabidopsis. On the other hand, up-regulated genes related to protein phosphorylation and auto-ubiquitination processes were over-represented in C. bungeana but not in Arabidopsis.

Conclusions: We conducted the first deep-sequencing transcriptome profiling and chilling stress regulatory network analysis of C. bungeana, a subnival alpine plant with inherited cold tolerance. Comparative transcriptome analysis suggests that cold acclimation is not a major chilling tolerance mechanism of C. bungeana. Activation of protein phosphorylation and ubiquitination may confer chilling tolerance to C. bungeana in a more rapid and flexible way than cold acclimation. Such differences may have contributed to the differences in cold tolerance between C. bungeana and Arabidopsis. The results presented in this paper will be informative for gene discovery and the molecular mechanisms related to plant cold tolerance.

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Figures

Figure 1
Figure 1
Functional classifications of GO terms of allC. bungeanaunigenes.
Figure 2
Figure 2
Expression analysis of top 20 up-regulated DEGs by qPCR.
Figure 3
Figure 3
Biological process network of over-representative GO terms of chilling up-regulated DEGs. A, C. bungeana; B, ATH-SR; C, ATH-MA. Node size represented gene number in node and node filled color represented p value. White nodes were not significant over-representative terms. End nodes were indicated by green border and blue label. (i) cluster of “regulation processes”; (ii) cluster of “stimulus responses”; (iii) cluster of “metabolism processes”.
Figure 4
Figure 4
Molecular function network of over-representative GO terms of chilling up-regulated DEGs.A, C. bungeana; B, ATH-SR; C, ATH-MA. Node size represented gene number in node and node filled color represented p value. White nodes were not significant over-representative terms. End nodes were indicated by green border and blue label.
Figure 5
Figure 5
Analysis of chilling up-regulated TFs. A. Venn diagram of chilling up-regulated TFs in C. bungeana and Arabidopsis. B. Classification of chilling up-regulated transcription factors of C. bungeana by family.
Figure 6
Figure 6
Classification of chilling up-regulated protein kinases of C. bungeana by family.
Figure 7
Figure 7
KEGG pathway network of chilling up-regulated DEGs. A, C. bungeana; B, ATH-SR; C, ATH-MA. Node size represented gene number in node and node filled color represented p value.
Figure 8
Figure 8
Biological process network of over-representative GO terms of chilling stress down-regulated DEGs. A, C. bungeana; B, ATH-SR; C, ATH-MA. Node size represented gene number in node and node filled color represented p value. White nodes were not significant over-representative terms. End nodes were indicated by green border and blue label.
Figure 9
Figure 9
Molecular function network of over-representative GO terms of chilling stress down-regulated DEGs.A, C. bungeana; B, ATH-SR; C, ATH-MA. Node size represented gene number in node and node filled color represented p value. White nodes were not significant over-representative terms. End nodes were indicated by green border and blue label.
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References

    1. Fu XY, Chang JF, An LZ, Zhang MX, Xu SJ, Chen T, Liu YH, Xin H, Wang JH. Association of the cold-hardiness of Chorispora bungeana with the distribution and accumulation of calcium in the cells and tissues. Environ Exp Bot. 2006;55:282–293. doi: 10.1016/j.envexpbot.2004.11.009. - DOI
    1. Liu YJ, Zhao ZG, Si J, Di CX, Han J, An LZ. Brassinosteroids alleviate chilling-induced oxidative damage by enhancing antioxidant defense system in suspension cultured cells of Chorispora bungeana. Plant Growth Regul. 2009;59:207–214. doi: 10.1007/s10725-009-9405-9. - DOI
    1. Shi Y, An L, Zhang M, Huang C, Zhang H, Xu S. Regulation of the plasma membrane during exposure to low temperatures in suspension-cultured cells from a cryophyte (Chorispora bungeana) Protoplasma. 2008;232:173–181. doi: 10.1007/s00709-008-0291-1. - DOI - PubMed
    1. Guo FX, Zhang MX, Chen Y, Zhang WH, Xu SJ, Wang JH, An LZ. Relation of several antioxidant enzymes to rapid freezing resistance in suspension cultured cells from alpine Chorispora bungeana. Cryobiology. 2006;52:241–250. doi: 10.1016/j.cryobiol.2005.12.001. - DOI - PubMed
    1. Ding S, Huang CL, Sheng HM, Song CL, Li YB, An LZ. Effect of inoculation with the endophyte Clavibacter sp. strain Enf12 on chilling tolerance in Chorispora bungeana. Physiol Plant. 2011;141:141–151. doi: 10.1111/j.1399-3054.2010.01428.x. - DOI - PubMed

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