| Summary: | <p>Abstract</p> <p>Background</p> <p>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. <it>Chorispora bungeana</it> 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 <it>C. bungeana</it> seedlings were analyzed by Illumina deep-sequencing and compared with Arabidopsis.</p> <p>Results</p> <p>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 <it>de novo</it> 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 <it>C. bungeana</it> and Arabidopsis responding to chilling. Karrikins were found as new plant growth regulators involved in chilling responses of <it>C. bungeana</it> and Arabidopsis. However, genes involved in cold acclimation were enriched in chilling up-regulated genes in Arabidopsis but not in <it>C. bungeana.</it> In addition, although transcription activations were stimulated in both <it>C. bungeana</it> and Arabidopsis, no <it>CBF</it> putative ortholog was up-regulated in <it>C. bungeana</it> while <it>CBF2</it> and <it>CBF3</it> 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 <it>C. bungeana</it> but not in Arabidopsis.</p> <p>Conclusions</p> <p>We conducted the first deep-sequencing transcriptome profiling and chilling stress regulatory network analysis of <it>C. bungeana</it>, a subnival alpine plant with inherited cold tolerance. Comparative transcriptome analysis suggests that cold acclimation is not a major chilling tolerance mechanism of <it>C. bungeana</it>. Activation of protein phosphorylation and ubiquitination may confer chilling tolerance to <it>C. bungeana</it> in a more rapid and flexible way than cold acclimation. Such differences may have contributed to the differences in cold tolerance between <it>C. bungeana</it> and Arabidopsis. The results presented in this paper will be informative for gene discovery and the molecular mechanisms related to plant cold tolerance.</p>
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