Global transcriptome profiles of Camellia sinensis during cold acclimation

Xin-Chao Wang 1 Qiong-Yi Zhao 0 2 Chun-Lei Ma 1 Zong-Hong Zhang 2 Hong-Li Cao 1 Yi-Meng Kong 0 Chuan Yue 1 Xin-Yuan Hao 1 Liang Chen 1 Jian-Qiang Ma 1 Ji-Qiang Jin 1 Xuan Li 0 Ya-Jun Yang 1 0 Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences Chinese Academy of Sciences , Shanghai 200032 , China 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 The University of Queensland, Queensland Brain Institute , Qld 4072 , Australia - Global transcriptome Wang et al. Open Access Global transcriptome profiles of Camellia sinensis during cold acclimation 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. Background Low temperatures are one of the most important environmental factors that temperate plants have to cope with during their life cycles. Some plants can enhance their freezing tolerance after exposure to low but non-freezing temperatures for a period of time, a process known as cold acclimation (CA) [1]. CA is a complex process that involves cellular, physiological, metabolic and molecular modifications. When plants sense the cold temperature, a series of protective mechanisms are triggered [2-4]. These include resetting the cellular framework; alternating the composition, structure and function of the plasma membrane; synthesizing cryoprotectant molecules such as soluble sugars, sugar alcohols and low-molecular-weight nitrogenous compounds; decreasing the ratio of free water content; improving the scavenging activity of reactive oxygen species (ROS); and introducing antifreeze proteins. These alterations help plants maintain a metabolic balance of substance and energy in cold environments. A group of cold-related genes has been reported to regulate these aforementioned changes [2-7]. Moreover, changes in gene expression have been demonstrated to occur during CA in a wide range of plant species, and hundreds of cold inducible genes have been identified [8]. Tea is the most popular non-alcoholic health beverage in the world, and the tea plant (Camellia sinensis (L.) O. Kuntze) is one of the most important economic crops in China, India, Sri Lanka, Kenya, among others [9]. As an evergreen woody plant, the tea plant can be grown in tropical to subtropical climates. Due to the local climate changes, tea plants have to cope with low temperatures during the wintertime. Low temperatures are one of the most critical environmental factors that limit its growth, survival and geographical distribution [10]. Thus, finding ways to improve tea plants resistance to low temperatures is of great importance. Like other perennial evergreen woody crops, during the CA process, the cold tolerance of tea plants enhances with the decrease in temperature and reduces with the increase in temperature. A previous study showed that when the average air temperature decreases to around 7C, tea plants undergo the CA process, and after the average air temperature increases to over 9C, tea plants start the de-acclimation process [11]. There are few studies that have focused on the cellular, physiological and metabolic changes during CA in tea plants. When tea plants undergo the CA process, the thickness of palisade tissue is increased and the stability of plasma membrane is enhanced. In addition, the concentration of the cytochylema and ratio of bound water in the cytoplasm, the amount of unsaturated fatty acids and total proteins in the plasma membrane, and the content of soluble proteins in the leaf are also increased. Meanwhile, the activities of some detoxification enzymes, such as catalase (CAT), superoxide dismutase (SOD), peroxidase (POD) and esterase (EST) are increased, whereas the metabolic activity is decreased [11,12]. Some cold-induced genes have been cloned in tea plants [13,14]. As a complex biological phenomenon, the ability of tea plants to resist the cold is regulated by a series of genes involved in a complex regulatory network [15]. Using an omics research strategy to understand the mechanism of CA in tea plants is the key to improving tea productivity and geographical distribution. RNA-Seq is a recently developed approach using a massively parallel sequencing strategy to generate transcriptome profiles. It has emerged as a cost-effective approach for high-throughput sequence determination and has unprecedentedly improved the efficiency and speed of gene discovery [16,17]. Digital gene expression (DGE) is a tag-based sequencing approach according to which short tags are generated by endonuclease. The expression level of genes in the sample is measured by counting the number of tags generated from each transcript [18]. This study demonstrates the first attempt to use a combination of RNA-Seq and DGE to study the transcriptome profiles in tea plants and thereby gain a deeper insight into the molecular mechanism of CA. The resulting transcriptome profiles from tea plants not only contributes to the in-depth knowledge of the genes involved in CA but also improves our understanding of plant-environment interacti (...truncated)