Global transcriptome and gene regulation network for secondary metabolite biosynthesis of tea plant Camellia sinensisReport as inadecuate

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BMC Genomics

, 16:560

Plant genomics


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.

KeywordsTea plant Camellia sinensis RNA-seq Secondary metabolite Transcription factor Regulation network AbbreviationsC. sinensisCamellia sinensis

ESTExpressed sequence tag

RNA-seqRNA sequencing

1st leafFirst leaf

2nd leafSecond leaf

one and a budOne leaf and one bud

two and a budTwo leaves and one bud

bpBase pair

MbpMegabase pairs

GbpGigabase pairs

NCBINational Center for Biotechnology Information

NrNCBI non-redundant protein

TAIRThe Arabidopsis Information Resource

TrEMBLTranslated EMBL nucleotide sequence database

CDDConserved domain database

GOGene ontology

COGCluster of orthologous groups


KEGGKyoto encyclopedia of genes and genomes

PALPhenylalanine ammonia-lyase

C4HCinnamic acid 4-hydroxylase

4CL4-coumarate-CoA ligase

CHSChalcone synthase

CHIChalcone isomerase

F3HFlavanone 3-hydroxylase

F3′,5′HFlavonoid 3′,5′-hydroxylase

F3′HFlavonoid 3′-hydroxylase

FLSFlavonol synthase

DFRDihydroflavonol 4-reductase

ANSAnthocyanidin synthase

ANRAnthocyanidin reductase

LARLeucocyanidin reductase

FGSFlavan-3-ol gallate synthase

LDOXLeucoanthocyanidin oxidase

UFGTUDP-glucose: flavonoid 3-O-glucosyl transferase

AnaseAdenosine nucleosidase

APRTAdenine phosphoribosyltransferase

AMPDAMP deaminase

IMPDHIMP dehydrogenase


7-NMT7-methylxanthosine synthase


MXMTTheobromine synthase

TCSTea caffeine synthase

GSGlutamine synthetase


ALTAlanine aminotransferase

ADCArginine decarboxylase

TSTheanine synthetase

qRT-PCRQuantitative real-time PCR

TFTranscription factor

AtTFDBArabidopsis transcription factor database

Chun-Fang Li and Yan Zhu contributed equally to this work.

Electronic supplementary materialThe online version of this article doi:10.1186-s12864-015-1773-0 contains supplementary material, which is available to authorized users.

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Author: Chun-Fang Li - Yan Zhu - Yao Yu - Qiong-Yi Zhao - Sheng-Jun Wang - Xin-Chao Wang - Ming-Zhe Yao - Da Luo - Xuan Li - Lian



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