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

Abstract

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.

L-Theanine Content and Related Gene Expression: Novel Insights into Theanine Biosynthesis and Hydrolysis among Different Tea Plant (Camellia sinensis L.) Tissues and Cultivars

“…At present, a few studies about the enzymes involved in the theanine metabolism pathway at gene level have been reported (Shi et al, 2011; Li et al, 2015b). To better understand the theanine metabolic mechanism at molecular level and provide references for identification and breeding of high theanine tea plant resources, it is essential to explore the correlations between theanine metabolic related genes and contents.…”

Comparative Transcriptome Analysis of Chinary, Assamica and Cambod tea (Camellia sinensis) Types during Development and Seasonal Variation using RNA-seq Technology

“…The amount of catechins present in the tea shoots gives an indication of the potential of a cultivar to produce good quality tea. Recently, RNA-Seq technology was used to identify key genes involved in the regulation of the flavonoid biosynthesis pathway in tea1130. However, only few reports are available on the changes of genes related to catechin biosynthesis in response to environmental stresses3132.…”

“…Due to non-availability of the reference genome sequence in tea, informations generated are not comprehensive. Recently, attempts have been made to identify transcriptional regulation using transcriptomic approach in tea191011. However, these studies are limited to either specific cultivar and/or seasons.…”

Gene expression analysis of bud and leaf color in tea

“…Recently, RNA-Seq method of high-throughput sequencing technology has been widely used to explore the potential mechanisms associated with important traits in C. sinensis (Paul et al, 2014;Li et al, 2015;Shi et al, 2015;Tai et al, 2015;Wei et al, 2015;Wang et al, 2016;Wu et al, 2016;Zhang et al, 2016). This method allows a comparison of the whole transcriptome of samples with large difference in certain trait or under treatments.…”