Gene co-expression network analysis reveals coordinated regulation of three characteristic secondary biosynthetic pathways in tea plant (Camellia sinensis).
ABSTRACT: The leaves of tea plants (Camellia sinensis) are used to produce tea, which is one of the most popular beverages consumed worldwide. The nutritional value and health benefits of tea are mainly related to three abundant characteristic metabolites; catechins, theanine and caffeine. Weighted gene co-expression network analysis (WGCNA) is a powerful system for investigating correlations between genes, identifying modules among highly correlated genes, and relating modules to phenotypic traits based on gene expression profiling. Currently, relatively little is known about the regulatory mechanisms and correlations between these three secondary metabolic pathways at the omics level in tea.In this study, levels of the three secondary metabolites in ten different tissues of tea plants were determined, 87,319 high-quality unigenes were assembled, and 55,607 differentially expressed genes (DEGs) were identified by pairwise comparison. The resultant co-expression network included 35 co-expression modules, of which 20 modules were significantly associated with the biosynthesis of catechins, theanine and caffeine. Furthermore, we identified several hub genes related to these three metabolic pathways, and analysed their regulatory relationships using RNA-Seq data. The results showed that these hub genes are regulated by genes involved in all three metabolic pathways, and they regulate the biosynthesis of all three metabolites. It is notable that light was identified as an important regulator for the biosynthesis of catechins.Our integrated omics-level WGCNA analysis provides novel insights into the potential regulatory mechanisms of catechins, theanine and caffeine metabolism, and the identified hub genes provide an important reference for further research on the molecular biology of tea plants.
Project description:BACKGROUND:Catechins, caffeine, and theanine as three important metabolites in the tea leaves play essential roles in the formation of specific taste and shows potential health benefits to humans. However, the knowledge on the dynamic changes of these metabolites content over seasons, as well as the candidate regulatory factors, remains largely undetermined. RESULTS:An integrated transcriptomic and metabolomic approach was used to analyze the dynamic changes of three mainly metabolites including catechins, caffeine, and theanine, and to explore the potential influencing factors associated with these dynamic changes over the course of seasons. We found that the catechins abundance was higher in Summer than that in Spring and Autumn, and the theanine abundance was significantly higher in Spring than that in Summer and Autumn, whereas caffeine exhibited no significant changes over three seasons. Transcriptomics analysis suggested that genes in photosynthesis pathway were significantly down-regulated which might in linkage to the formation of different phenotypes and metabolites content in the tea leaves of varied seasons. Fifty-six copies of nine genes in catechins biosynthesis, 30 copies of 10 genes in caffeine biosynthesis, and 12 copies of six genes in theanine biosynthesis were detected. The correlative analysis further presented that eight genes can be regulated by transcription factors, and highly correlated with the changes of metabolites abundance in tea-leaves. CONCLUSION:Sunshine intensity as a key factor can affect photosynthesis of tea plants, further affect the expression of major Transcription factors (TFs) and structural genes in, and finally resulted in the various amounts of catechins, caffeine and theaine in tea-leaves over three seasons. These findings provide new insights into abundance and influencing factors of metabolites of tea in different seasons, and further our understanding in the formation of flavor, nutrition and medicinal function.
Project description:Tea plants (Camellia sinensis) are used to produce one of the most important beverages worldwide. The nutritional value and healthful properties of tea are closely related to the large amounts of three major characteristic constituents including polyphenols (mainly catechins), theanine and caffeine. Although oil tea (Camellia oleifera) belongs to the genus Camellia, this plant lacks these three characteristic constituents. Comparative analysis of tea and oil tea via RNA-Seq would help uncover the genetic components underlying the biosynthesis of characteristic metabolites in tea.We found that 3,787 and 3,359 bud genes, as well as 4,042 and 3,302 leaf genes, were up-regulated in tea and oil tea, respectively. High-performance liquid chromatography (HPLC) analysis revealed high levels of all types of catechins, theanine and caffeine in tea compared to those in oil tea. Activation of the genes involved in the biosynthesis of these characteristic compounds was detected by RNA-Seq analysis. In particular, genes encoding enzymes involved in flavonoid, theanine and caffeine pathways exhibited considerably different expression levels in tea compared to oil tea, which were also confirmed by quantitative RT-PCR (qRT-PCR).We assembled 81,826 and 78,863 unigenes for tea and oil tea, respectively, based on their differences at the transcriptomic level. A potential connection was observed between gene expression and content variation for catechins, theanine and caffeine in tea and oil tea. The results demonstrated that the metabolism was activated during the accumulation of characteristic metabolites in tea, which were present at low levels in oil tea. From the molecular biological perspective, our comparison of the transcriptomes and related metabolites revealed differential regulatory mechanisms underlying secondary metabolic pathways in tea versus oil tea.
Project description:Plant hormones play an important role in the chemical metabolism of postharvest plants. However, alterations in plant hormones of postharvest tea and their potential modulation of quality-related metabolites are unknown. In this study, the dynamic alterations of abscisic acid (ABA), salicylic acid (SA), jasmonic acid (JA), and critical metabolites, such as catechins, theanine, and caffeine, in tea leaves were analyzed during withering from 0 to 24 h. It was found that the ABA content increased from 0 to 9 h but decreased thereafter, JA continuously increased, and the SA content showed no significant change. With the exception of gallocatechin (GC) and epicatechin (EC), the amounts of other critical components were significantly reduced at 24 h. Transcriptome analysis showed that compared with 0 h, 2256, 3654, and 1275 differentially expressed genes (DEGs) were identified at 9, 15, and 24 h, respectively. For all comparisons, DEGs corresponding to the pathways of "phenylalanine, tyrosine, and tryptophan biosynthesis" and "phenylalanine metabolism", involved in the biosynthesis of catechins, were significantly enriched. Weighted correlation network analysis (WGCNA) of co-expression genes indicated that many of the modules were only correlated with a specific trait during the withering process; the dark olive-green module, however, was correlated with two traits, ABA and theanine. Our study indicates that withering induced dramatic alterations in gene transcription as well as levels of hormones (ABA, JA, and SA) and important components, and that ABA regulated theanine metabolism during this process.
Project description:Rising CO<sub>2</sub> concentration, a driving force of climate change, is impacting global food security by affecting plant physiology. Nevertheless, the effects of elevated CO<sub>2</sub> on primary and secondary metabolism in tea plants (Camellia sinensis L.) still remain largely unknown. Here we showed that exposure of tea plants to elevated CO<sub>2</sub> (800 µmol mol<sup>-1</sup> for 24 d) remarkably improved both photosynthesis and respiration in tea leaves. Furthermore, elevated CO<sub>2</sub> increased the concentrations of soluble sugar, starch and total carbon, but decreased the total nitrogen concentration, resulting in an increased carbon to nitrogen ratio in tea leaves. Among the tea quality parameters, tea polyphenol, free amino acid and theanine concentrations increased, while the caffeine concentration decreased after CO<sub>2</sub> enrichment. The concentrations of individual catechins were altered differentially resulting in an increased total catechins concentration under elevated CO<sub>2</sub> condition. Real-time qPCR analysis revealed that the expression levels of catechins and theanine biosynthetic genes were up-regulated, while that of caffeine synthetic genes were down-regulated in tea leaves when grown under elevated CO<sub>2</sub> condition. These results unveiled profound effects of CO<sub>2</sub> enrichment on photosynthesis and respiration in tea plants, which eventually modulated the biosynthesis of key secondary metabolites towards production of a quality green tea.
Project description:To investigate the relationships between hormones and critical components in tea leaves during withering process, we detected the alterations of abscisic acid (ABA), salicylic acid (SA), and jasmonic acid (JA), catechins, theanine, and caffeine in tea leaves withered at different time points from 0 to 24 hours. The content of ABA increased from 0h to 9h and decreased thereafter and JA content continuous increased, however, SA content was no significantly changes during withering process. Except for gallocatechin (GC) and epicatechin (EC), the contents of other critical components were significantly reduced at 24h. Transcriptome analysis shown that compared with 0h, a total of 2,256, 3,654, and 1,275 differentially expressed genes (DEGs) were identified at 9h, 15h, and 24h, respectively. The pathways of“Phenylalanine, tyrosine and tryptophan biosynthesis”, and “Phenylalanine metabolism” involved in biosynthesis of catechins were enriched significantly with DEGs of all comparisons. Weighted correlation network analysis (WGCNA) of co-expression genes indicated that many of modules were correlated with a specific trait only, however, the darkolivegreen module were correlated with two traits ABA and theanine during withering process. Our study indicates that withering induced dramatic alteration of the gene transcription, hormones (ABA, JA, and SA) and important components, and ABA may regulate theanine matebolism during this process. Overall design: The expression profiles of mRNAs during withering process
Project description:The tea plant [Camellia sinensis (L.) O. Kuntze] is an important commercial crop rich in bioactive ingredients, especially catechins, caffeine, theanine and other free amino acids, which the quality of tea leaves depends on. Drought is the most important environmental stress affecting the yield and quality of this plant. In this study, the effects of drought stress on the phenotype, physiological characteristics and major bioactive ingredients accumulation of C. sinensis leaves were examined, and the results indicated that drought stress resulted in dehydration and wilt of the leaves, and significant decrease in the total polyphenols and free amino acids and increase in the total flavonoids. In addition, HPLC analysis showed that the catechins, caffeine, theanine and some free amino acids in C. sinensis leaves were significantly reduced in response to drought stress, implying that drought stress severely decreased the quality of C. sinensis leaves. Furthermore, differentially expressed genes (DEGs) related to amino acid metabolism and secondary metabolism were identified and quantified in C. sinensis leaves under drought stress using high-throughput Illumina RNA-Seq technology, especially the key regulatory genes of the catechins, caffeine, and theanine biosynthesis pathways. The expression levels of key regulatory genes were consistent with the results from the HPLC analysis, which indicate a potential molecular mechanism for the above results. Taken together, these data provide further insights into the mechanisms underlying the change in the quality of C. sinensis leaves under environmental stress, which involve changes in the accumulation of major bioactive ingredients, especially catechins, caffeine, theanine and other free amino acids.
Project description:Tea (Camellia sinensis (L.) O. Kuntze), one of the main crops in China, is high in various bioactive compounds including flavonoids, catechins, caffeine, theanine, and other amino acids. C. sinensis is also known as an accumulator of fluoride (F), and the bioactive compounds are affected by F, however, the mechanism remains unclear. Here, the effects of F treatment on the accumulation of F and major bioactive compounds and gene expression were investigated, revealing the molecular mechanisms affecting the accumulation of bioactive compounds by F treatment. The results showed that F accumulation in tea leaves gradually increased under exogenous F treatments. Similarly, the flavonoid content also increased in the F treatment. In contrast, the polyphenol content, free amino acids, and the total catechins decreased significantly. Special amino acids, such as sulfur-containing amino acids and proline, had the opposite trend of free amino acids. Caffeine was obviously induced by exogenous F, while the theanine content peaked after two day-treatment. These results suggest that the F accumulation and content of bioactive compounds were dramatically affected by F treatment. Furthermore, differentially expressed genes (DEGs) related to the metabolism of main bioactive compounds and amino acids, especially the pivotal regulatory genes of catechins, caffeine, and theanine biosynthesis pathways, were identified and analyzed using high-throughput Illumina RNA-Seq technology and qRT-PCR. The expression of pivotal regulatory genes is consistent with the changes of the main bioactive compounds in C. sinensis leaves, indicating a complicated molecular mechanism for the above findings. Overall, these data provide a reference for exploring the possible molecular mechanism of the accumulation of major bioactive components such as flavonoid, catechins, caffeine, theanine and other amino acids in tea leaves in response to fluoride treatment.
Project description:The tea cultivar 'Xiaoxueya', a temperature-sensitive albino mutant, is a rare tea germplasm because of its highly enriched amino acid content and brisk flavour. In comparison with green leaf tissues of 'Xiaoxueya', albino leaves show significant deficiency in chlorophylls and carotenoids and severely disrupted chloroplasts. Furthermore, the accumulation of quality-related secondary metabolites is altered in 'Xiaoxueya' albino leaf, with significantly increased contents of total amino acids, theanine, and glutamic acid and significantly decreased contents of alkaloids, catechins, and polyphenols. To uncover the molecular mechanisms underlying albinism and quality-related constituent variation in 'Xiaoxueya' leaves, expression profiles of pivotal genes involved in the biosynthetic pathways of pigments, caffeine, theanine, and catechins were investigated by quantitative real-time PCR technology. The results revealed that suppressed expression of the chloroplast-localized 1-deoxy-D-xylulose-5-phosphate synthase genes DXS1 and DXS2 involved in the 2-C-methyl-D-erythritol-4-phosphate (MEP) pathway and protochlorophyllide oxidoreductase genes POR1 and POR2 involved in the chlorophyll biosynthetic pathway is responsible for the pigment deficiency in 'Xiaoxueya' albino leaf. Additionally, the low expression of the tea caffeine synthase gene (TCS) involved in caffeine biosynthesis and the chalcone synthase genes CHS1, CHS2, and CHS3, the chalcone isomerase gene CHI, the flavonoid 3',5'-hydroxylase genes F3'5'H1 and F3'5'H2, and the anthocyanidin reductase genes ANR1 and ANR2 involved in the flavonoid pathway is related to the reduction in alkaloid and catechin levels in 'Xiaoxueya' albino leaves.
Project description:Tea, one of the world's most important beverage crops, provides numerous secondary metabolites that account for its rich taste and health benefits. Here we present a high-quality sequence of the genome of tea, Camellia sinensis var. sinensis (CSS), using both Illumina and PacBio sequencing technologies. At least 64% of the 3.1-Gb genome assembly consists of repetitive sequences, and the rest yields 33,932 high-confidence predictions of encoded proteins. Divergence between two major lineages, CSS and Camellia sinensis var. assamica (CSA), is calculated to ?0.38 to 1.54 million years ago (Mya). Analysis of genic collinearity reveals that the tea genome is the product of two rounds of whole-genome duplications (WGDs) that occurred ?30 to 40 and ?90 to 100 Mya. We provide evidence that these WGD events, and subsequent paralogous duplications, had major impacts on the copy numbers of secondary metabolite genes, particularly genes critical to producing three key quality compounds: catechins, theanine, and caffeine. Analyses of transcriptome and phytochemistry data show that amplification and transcriptional divergence of genes encoding a large acyltransferase family and leucoanthocyanidin reductases are associated with the characteristic young leaf accumulation of monomeric galloylated catechins in tea, while functional divergence of a single member of the glutamine synthetase gene family yielded theanine synthetase. This genome sequence will facilitate understanding of tea genome evolution and tea metabolite pathways, and will promote germplasm utilization for breeding improved tea varieties.
Project description:Senescence is initiated immediately in harvested tea leaves, and leads to physiological and biochemical changes, and could affects the final tea products. In the present work, we investigated the relationship between hormones and critical components in harvested tea leaves before withering, changes in hormones including abscisic acid (ABA), salicylic acid (SA), jasmonic acid (JA), and critical components like catechins, theanine, and caffeine were analyzed. Significant changes in these substances were identified and ABA correlated with catechin in harvested tea leaves before withering. RNA-seq transcriptome analysis revealed dramatic differences between tea samples at 1 h and 2 h compared with those at 0 h. The patterns of these three critical components correlated with the expression profiles of differentially expressed genes (DEGs). Weighted correlation network analysis of co-expressed genes revealed that genes in the mediumpurple2 module correlated with ABA and catechins. The results of this study suggest that harvested tea leaves before withering undergo significant hormonal changes (ABA, JA, and SA) and ABA may participate in regulating catechin biosynthesis. Overall design: mRNA profiles of tea leaves at 0, 1 and 2 hours after harvested