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Open Access Highly Accessed Research article

Global transcriptome profiles of Camellia sinensis during cold acclimation

Xin-Chao Wang1, Qiong-Yi Zhao23, Chun-Lei Ma1, Zong-Hong Zhang3, Hong-Li Cao1, Yi-Meng Kong2, Chuan Yue1, Xin-Yuan Hao1, Liang Chen1, Jian-Qiang Ma1, Ji-Qiang Jin1, Xuan Li2* and Ya-Jun Yang1*

Author Affiliations

1 Tea Research Institute, Chinese Academy of Agricultural Sciences; National Center for Tea Improvement, Key Laboratory of Tea Plant Biology and Resources Utilization, Ministry of Agriculture, Hangzhou 310008, China

2 Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai 200032, China

3 The University of Queensland, Queensland Brain Institute, Qld 4072, Australia

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BMC Genomics 2013, 14:415  doi:10.1186/1471-2164-14-415

Published: 22 June 2013

Abstract

Background

Tea is the most popular non-alcoholic health beverage in the world. The tea plant (Camellia sinensis (L.) O. Kuntze) needs to undergo a cold acclimation process to enhance its freezing tolerance in winter. Changes that occur at the molecular level in response to low temperatures are poorly understood in tea plants. To elucidate the molecular mechanisms of cold acclimation, we employed RNA-Seq and digital gene expression (DGE) technologies to the study of genome-wide expression profiles during cold acclimation in tea plants.

Results

Using the Illumina sequencing platform, we obtained approximately 57.35 million RNA-Seq reads. These reads were assembled into 216,831 transcripts, with an average length of 356 bp and an N50 of 529 bp. In total, 1,770 differentially expressed transcripts were identified, of which 1,168 were up-regulated and 602 down-regulated. These include a group of cold sensor or signal transduction genes, cold-responsive transcription factor genes, plasma membrane stabilization related genes, osmosensing-responsive genes, and detoxification enzyme genes. DGE and quantitative RT-PCR analysis further confirmed the results from RNA-Seq analysis. Pathway analysis indicated that the “carbohydrate metabolism pathway” and the “calcium signaling pathway” might play a vital role in tea plants’ responses to cold stress.

Conclusions

Our study presents a global survey of transcriptome profiles of tea plants in response to low, non-freezing temperatures and yields insights into the molecular mechanisms of tea plants during the cold acclimation process. It could also serve as a valuable resource for relevant research on cold-tolerance and help to explore the cold-related genes in improving the understanding of low-temperature tolerance and plant-environment interactions.

Keywords:
Camellia Sinensis; Cold Acclimation; RNA-Seq; DGE; Genome-wide Expression Profiles; Tea Plants