Global transcriptome and gene regulation network for secondary metabolite biosynthesis of tea plant (Camellia sinensis)

BMC Genomics, Jul 2015

Background Major 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. Results RNA 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. Conclusions Our 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.

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Global transcriptome and gene regulation network for secondary metabolite biosynthesis of tea plant (Camellia sinensis)

Li et al. BMC Genomics Global transcriptome and gene regulation network for secondary metabolite biosynthesis of tea plant (Camellia sinensis) Chun-Fang Li 0 2 3 Yan Zhu 0 1 3 Yao Yu 1 3 Qiong-Yi Zhao 1 3 5 Sheng-Jun Wang 3 4 Xin-Chao Wang 2 3 Ming-Zhe Yao 2 3 Da Luo 3 6 Xuan Li 1 3 Liang Chen 2 3 Ya-Jun Yang 2 3 0 Equal contributors 1 Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences , Shanghai 200032 , China 2 Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Tea Research Institute of the Chinese Academy of Agricultural Sciences , Hangzhou 310008 , China 3 mail.tricaas.com 4 Suzhou Genezym Biological Technology Co, Ltd , Suzhou 215011 , China 5 Present address: The University of Queensland, Queensland Brain Institute , Brisbane St Lucia QLD 4072 , Australia 6 School of Life Sciences, Sun Yat-Sen University , Guangzhou 510275 , China Background: Major 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. Results: RNA 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. Conclusions: Our 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. Tea plant; Camellia sinensis; RNA-seq; Secondary metabolite; Transcription factor; Regulation network - Background The production of secondary metabolites in tea plants (Camellia sinensis (L.) O. Kuntze) contributes to the rich flavors, clean taste, and nutrient content of tea [1, 2], one of the most popular beverages worldwide. These secondary metabolites are also known to be beneficial to human health. Animal, clinical, and epidemiological studies suggest that tea is beneficial in the prevention and treatment of chronic diseases, including cardiovascular diseases and cancer [3–5]. The secondary metabolites in tea plants include polyphenols, alkaloids, volatile oils, and others. Among them, flavonoids, caffeine, and theanine are the major constituents. Flavonoids are phenylalanine-derived, physiologically active secondary metabolites, and include flavones, flavonols, isoflavones, flavanones, flavanols, and anthocyanidins [6]. These compounds have a wide range of functions, such as antioxidant activity, ultraviolet light protection, and defense against phytopathogens. Caffeine is a purine alkaloid that has been widely used as a stimulant and an ingredient in drugs. Caffeine accumulates in seeds, buds, and young leaves, and serves as an anti-herbivory compound to protect soft tissues from predators [7]. Caffeine in seed coats is released into the soil and inhibits the germination of other seeds [8]. Theanine is a unique free amino acid and accounts for approximately 50 % of the total free amino acids (...truncated)


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Chun-Fang Li, Yan Zhu, Yao Yu, Qiong-Yi Zhao, Sheng-Jun Wang, Xin-Chao Wang, Ming-Zhe Yao, Da Luo, Xuan Li, Liang Chen, Ya-Jun Yang. Global transcriptome and gene regulation network for secondary metabolite biosynthesis of tea plant (Camellia sinensis), BMC Genomics, 2015, pp. 560, 16, DOI: 10.1186/s12864-015-1773-0