BackgroundMajor secondary metabolites, including flavonoids, caffeine, and theanine, are important components of tea products and are closely related to the taste, flavor, and health benefits of tea. Secondary metabolite biosynthesis in Camellia sinensis is differentially regulated in different tissues during growth and development. Until now, little was known about the expression patterns of genes involved in secondary metabolic pathways or their regulatory mechanisms. This study aimed to generate expression profiles for C. sinensis tissues and to build a gene regulation model of the secondary metabolic pathways.ResultsRNA sequencing was performed on 13 different tissue samples from various organs and developmental stages of tea plants, including buds and leaves of different ages, stems, flowers, seeds, and roots. A total of 43.7 Gbp of raw sequencing data were generated, from which 347,827 unigenes were assembled and annotated. There were 46,693, 8446, 3814, 10,206, and 4948 unigenes specifically expressed in the buds and leaves, stems, flowers, seeds, and roots, respectively. In total, 1719 unigenes were identified as being involved in the secondary metabolic pathways in C. sinensis, and the expression patterns of the genes involved in flavonoid, caffeine, and theanine biosynthesis were characterized, revealing the dynamic nature of their regulation during plant growth and development. The possible transcription factor regulation network for the biosynthesis of flavonoid, caffeine, and theanine was built, encompassing 339 transcription factors from 35 families, namely bHLH, MYB, and NAC, among others. Remarkably, not only did the data reveal the possible critical check points in the flavonoid, caffeine, and theanine biosynthesis pathways, but also implicated the key transcription factors and related mechanisms in the regulation of secondary metabolite biosynthesis.ConclusionsOur study generated gene expression profiles for different tissues at different developmental stages in tea plants. The gene network responsible for the regulation of the secondary metabolic pathways was analyzed. Our work elucidated the possible cross talk in gene regulation between the secondary metabolite biosynthetic pathways in C. sinensis. The results increase our understanding of how secondary metabolic pathways are regulated during plant development and growth cycles, and help pave the way for genetic selection and engineering for germplasm improvement.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1773-0) contains supplementary material, which is available to authorized users.

Tea plant (Camellia sinensis) is an economically important beverage crop. Drought stress (DS) seriously limits the growth and development of tea plant, thus affecting crop yield and quality. To elucidate the molecular mechanisms of tea plant responding to DS, we performed transcriptomic analysis of tea plant during the three stages [control (CK) and during DS, and recovery (RC) after DS] using RNA sequencing (RNA-Seq). Totally 378.08 million high-quality trimmed reads were obtained and assembled into 59,674 unigenes, which were extensively annotated. There were 5,955 differentially expressed genes (DEGs) among the three stages. Among them, 3,948 and 1,673 DEGs were up-regulated under DS and RC, respectively. RNA-Seq data were further confirmed by qRT-PCR analysis. Genes involved in abscisic acid (ABA), ethylene, and jasmonic acid biosynthesis and signaling were generally up-regulated under DS and down-regulated during RC. Tea plant potentially used an exchange pathway for biosynthesis of indole-3-acetic acid (IAA) and salicylic acid under DS. IAA signaling was possibly decreased under DS but increased after RC. Genes encoding enzymes involved in cytokinin synthesis were up-regulated under DS, but down-regulated during RC. It seemed probable that cytokinin signaling was slightly enhanced under DS. In total, 762 and 950 protein kinases belonging to 26 families were differentially expressed during DS and RC, respectively. Overall, 547 and 604 transcription factor (TF) genes belonging to 58 families were induced in the DS vs. CK and RC vs. DS libraries, respectively. Most members of the 12 TF families were up-regulated under DS. Under DS, genes related to starch synthesis were down-regulated, while those related to starch decomposition were up-regulated. Mannitol, trehalose and sucrose synthesis-related genes were up-regulated under DS. Proline was probably mainly biosynthesized from glutamate under DS and RC. The mechanism by which ABA regulated stomatal movement under DS and RC was partly clarified. These results document the global and novel responses of tea plant during DS and RC. These data will serve as a valuable resource for drought-tolerance research and will be useful for breeding drought-resistant tea cultivars.

Tea plant (Camellia sinensis (L.) O. Kuntze) originated from China, where distributed abundant genetic resources. It is of critical importance to well understanding of genetic diversity and population structure for effective collection, conservation, and utilization of tea germplasms. In this study, 96 new polymorphic EST-SSR markers were developed and used to analyze 450 tea accessions collected from 14 tea-producing regions across China. A total of 409 alleles were observed, and the gene diversity (H) and polymorphic information content (PIC) were estimated to be averagely 0.64 and 0.61, respectively, across all the tested samples. The higher level of genetic diversity was observed in original regions like Guangxi, Yunnan, and Guizhou provinces. The allele number, H, and PIC showed decreasing trend when the region was more and more away from origin center of tea plant, which gave us implications on the spreading route of tea plant in China. The clustering of 450 samples both showed a clear separation according to their geographic origin based on either model simulation or genetic distance. The genetic differentiation was further analyzed among five inferred populations represented different eco-geographic regions. The lowest F st and the closest relationship were revealed between proximal populations, which indicated that gene exchanges occurred frequently between nearby regions than distance ones. The majority of genetic variation resulted from differentiation within population (81.36%) rather than among inferred (13.6%) and regional (5.04%) populations based on analysis of molecular variance. Our study also revealed that the lower diversity and simpler population structure were found in improved cultivars than wild teas and landraces, which indicated that genetic base of developed cultivars became narrow because of longstanding domestication and artificial selection. So more attentions should be focused to conserve and utilize the beneficial genes in wild teas and landraces to broaden genetic variation of new cultivars in future breeding of the tea plant.