Global transcriptome profiles of Camellia sinensis during cold acclimation

Abstract

BackgroundTea 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.ResultsUsing 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.ConclusionsOur 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.

Application of data analysis in cold stress: a case study of Nicotiana benthamiana

“…In these varieties, 1711 genes were upregulated while 1402 were downregulated, with 394 common genes (Winfield et al, 2010). In tea plant (Camellia sinensis), 1770 differentially expressed genes were reported; of these, 1168 were upregulated and 602 were downregulated under cold stress (Wang et al, 2013). In this study, we have identified a total of 5205 DEGs.…”

RNA-Seq Data Analysis for Studying Abiotic Stress in Horticultural Plants

“…Standard transcriptome annotation included BLAST alignments against the NCBI nonredundant (NR) database and the COG database as well as GO and KEGG annotations. However, in some works an extensive annotation has been done also by alignments against EST databases (Wang et al 2013b , d ;Lee et al 2013 ), the From Pertea et al ( 2003 ) TAIR10 database (Wang et al 2013d ), or the PlantGDB database ).…”

“…In the second case, researchers studied the transcriptomes of tropical or other cold-sensitive plants useful in biotechnology or horticulture. Among them has been Jatropha curcas L., an oil-rich tropical shrub with multiple uses, including biodiesel production (Wang et al 2013b ), Anthurium andraeanum , one of the most popular tropical fl owers (Tian et al 2013 ), and the tea plant Camellia sinensis (Wang et al 2013d ).…”

The Omics of Cold Stress Responses in Plants

“…Several techniques, such as DNA microarrays, Expressed Sequence Tags (ESTs), Serial Analysis of Gene Expression (SAGE), Digital Gene Expression (DGE) profi ling, and Next-Generation Sequencing (NGS)-based tools such as RNA sequencing (RNA-seq) are being exploited to capture and identify the differentially regulated genes during stress conditions in plants (Cramer et al 2011 ;Lister et al 2009 ;Wang et al 2013 ) (Table 6.2 ). It provides an in-depth knowledge of the global gene expression pattern of plant response to stress stimuli (Jung et al 2003 ).…”