title: Global transcriptome and gene regulation network for secondary metabolite biosynthesis of tea plant (Camellia sinensis).
abstract: 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.
authors.affiliation: Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China. lichunfang@tricaas.com.
authors.forename: Chun-Fang
authors.initials: CF
authors.lastname: Li
authors.affiliation: Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China. zhuyan@sibs.ac.cn.
authors.forename: Yan
authors.initials: Y
authors.lastname: Zhu
authors.affiliation: Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China. yyu01@sibs.ac.cn.
authors.forename: Yao
authors.initials: Y
authors.lastname: Yu
authors.affiliation: Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China. q.zhao@uq.edu.au.|Present address: The University of Queensland, Queensland Brain Institute, Brisbane St Lucia, QLD 4072, Australia. q.zhao@uq.edu.au.
authors.forename: Qiong-Yi
authors.initials: QY
authors.lastname: Zhao
authors.affiliation: Suzhou Genezym Biological Technology Co, Ltd, Suzhou, 215011, China. isi121@gmail.com.
authors.forename: Sheng-Jun
authors.initials: SJ
authors.lastname: Wang
authors.affiliation: Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China. xcw75@tricaas.com.
authors.forename: Xin-Chao
authors.initials: XC
authors.lastname: Wang
authors.affiliation: Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China. yaomz@tricaas.com.
authors.forename: Ming-Zhe
authors.initials: MZ
authors.lastname: Yao
authors.affiliation: School of Life Sciences, Sun Yat-Sen University, Guangzhou, 510275, China. luoda@mail.sysu.edu.cn.
authors.forename: Da
authors.initials: D
authors.lastname: Luo
authors.affiliation: Key Laboratory of Synthetic Biology, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China. lixuan@sippe.ac.cn.
authors.forename: Xuan
authors.initials: X
authors.lastname: Li
authors.affiliation: Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China. liangchen@mail.tricaas.com.
authors.forename: Liang
authors.initials: L
authors.lastname: Chen
authors.affiliation: Key Laboratory of Tea Biology and Resources Utilization, Ministry of Agriculture, Tea Research Institute of the Chinese Academy of Agricultural Sciences, Hangzhou, 310008, China. yjyang@mail.tricaas.com.
authors.forename: Ya-Jun
authors.initials: YJ
authors.lastname: Yang
mesh_terms: D053898:Biosynthetic Pathways / Q000235:genetics*; D002110:Caffeine / Q000096:biosynthesis; D028241:Camellia sinensis / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D005419:Flavonoids / Q000096:biosynthesis; D035264:Flowers / Q000235:genetics / Q000378:metabolism; D053263:Gene Regulatory Networks; D005971:Glutamates / Q000096:biosynthesis; D018515:Plant Leaves / Q000235:genetics / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D018517:Plant Roots / Q000235:genetics / Q000378:metabolism; D012313:RNA / Q000032:analysis; D060888:Real-Time Polymerase Chain Reaction; D017423:Sequence Analysis, RNA; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome
chemical_list: D005419:Flavonoids; D005971:Glutamates; D010940:Plant Proteins; D014157:Transcription Factors; D002110:Caffeine; D012313:RNA; C026166:theanine