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Flavonoids are the major class of characteristic secondary compounds in Camellia sinensis that affect quality of tea. However, the temporal variation and the underlying regulatory mechanism of flavonoid biosynthesis during different growth months require a further investigation. Here, we combined analyses of the metabolomics and transcriptomics to tea leaves freshly collected during five different months for a comprehensive understanding of flavonoid metabolism regulation in tea plants. Through loading plot analysis, significant changes in the contents of metabolites during growing months were discovered, and further co-expression and association analysis indicated that one flavone glycoside (naringenin-7-O-glucoside) and two flavonol glycosides (quercetin-3-O-galactoside and kaemferol-3-O-(6″-O-p-courmaroyl)-glucoside) were evaluated as growth markers, which may explain the high bitterness and astringency of August teas; additionally, the high levels of two flavan-3-ols (gallocatechin and catechin gallate) may contribute to the flavor formation of April tea. Meanwhile, multiple flavonoid-related structural genes, MYB and bHLH transcription factors exhibit specific expression patterns to modulate the biosynthesis of these key flavonoids. A co-expression regulatory sub-network was constructed based on profiles of differentially expressed genes; one CsbHLH and six transcription factors (three CsbHLHs and three CsMYBs) exhibited negative and positive roles in the regulation of flavonoid biosynthetic genes, respectively. Taken together, our results provide new insights into the regulation of principle flavonoids for unique flavor of tea regulated by many flavonoid-related structural genes and transcription factors during different growth months., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Background: Alternative splicing (AS) regulates mRNA at the post-transcriptional level to change gene function in organisms. However, little is known about the AS and its roles in tea plant (Camellia sinensis), widely cultivated for making a popular beverage tea., Results: In our study, the AS landscape and dynamics were characterized in eight tissues (bud, young leaf, summer mature leaf, winter old leaf, stem, root, flower, fruit) of tea plant by Illumina RNA-Seq and confirmed by Iso-Seq. The most abundant AS (~ 20%) was intron retention and involved in RNA processes. The some alternative splicings were found to be tissue specific in stem and root etc. Thirteen co-expressed modules of AS transcripts were identified, which revealed a similar pattern between the bud and young leaves as well as a distinct pattern between seasons. AS events of structural genes including anthocyanidin reductase and MYB transcription factors were involved in biosynthesis of flavonoid, especially in vegetative tissues. The AS isoforms rather than the full-length ones were the major transcripts involved in flavonoid synthesis pathway, and is positively correlated with the catechins content conferring the tea taste. We propose that the AS is an important functional mechanism in regulating flavonoid metabolites., Conclusion: Our study provides the insight into the AS events underlying tea plant's uniquely different developmental process and highlights the important contribution and efficacy of alternative splicing regulatory function to biosynthesis of flavonoids.

R2R3-MYB, bHLH, and WD40 proteins have been shown to control multiple enzymatic steps in the biosynthetic pathway responsible for the production of flavonoids, important secondary metabolites in Camellia sinensis. Few related transcription factor genes have been documented. The presence of R2R3-MYB, bHLH, and WD40 were statistically and bioinformatically analyzed on 127,094 C. sinensis transcriptome unigenes, resulting in identification of 73, 49, and 134 genes, respectively. C. sinensis phylogenetic trees were constructed for R2R3-MYB and bHLH proteins using previous Arabidopsis data and further divided into 27 subgroups (Sg) and 32 subfamilies. Motifs in some R2R3-MYB subgroups were redefined. Furthermore, Sg26 and Sg27 were expanded compared to Arabidopsis data, and bHLH proteins in C. sinensis were grouped into nine subfamilies. According to the functional annotation of Arabidopsis, flavonoid biosynthesis in C. sinensis was predicted to include R2R3-MYB genes in Sg4 (6), Sg5 (2), and Sg7 (1), as well as bHLH genes in subfamily 2 (2) and subfamily 24 (5). The wide evolutionary gap prevented phylogenetic analysis of WD40s; however, a single gene, CsWD40-1, was observed to share 80.4 % sequence homogeny with AtTTG1. Analysis of CsMYB4-1, CsMYB4-2, CsMYB4-3, CsMYB4-4, CsMYB5-1, and CsMYB5-2 revealed the interaction motif [DE]Lx2[RK]x3Lx6Lx3R, potentially contributing to the specificity of the bHLH partner in the stable MYB-bHLH complex. Full-length end-to-end polymerase chain reaction (PCR) and quantitative reverse transcriptase (qRT)-PCR were used to validate selected genes and generate relative expression ratio profiles in C. sinensis leaves by developmental stage and treatment conditions, including hormone and wound treatments. Potential target binding sites were predicted.

Abstract: Tea (Camellia sinensis) is a commercially important crop that contains valuable secondary metabolites. To understand the molecular regulation of secondary metabolism in tea, we selected and analyzed two cell lines of tea callus (Yunjing63Y and Yunjing63X) that showed different morphological characteristics and catechin contents. Yunjing63Y callus was yellow and tight, while yunjing63X callus was white and loose. HPLC analyses showed that Yunjing63Y contained 3.71 times higher levels of catechins than Yunjing63X. Using cDNA amplified fragment-length polymorphism (cDNA-AFLP) we identified 68 genes that were differentially expressed between the two lines. Of the 68 differentially expressed ESTs, 40 showed higher expressions in Yunjing63Y and 28 showed higher expressions in Yunjing63X. BLASTX comparisons classified these ESTs into seven functional groups; phenylpropanoid metabolism (2.9%), UDPG-dependent glucosyl transferase (8.8%), transcription factors (11.8%), transporters (13.2%), signal transduction (19.1%), other metabolism (26.5%), and unknown (17.7%). We used qRT-PCR to validate the expression of genes and ESTs, and found that genes associated with flavan-3-ols biosynthesis and metabolism were expressed at higher levels in Yunjing63Y than in Yunjing63X. In addition, the expression of ESTs associated with flavonoid biosynthesis, regulation and transport were higher in Yunjing63Y than in Yunjing63X. The full-length cDNA of a EST coding for a putative MYB transcription factor was amplified using rapid amplification of cDNA ends (RACE). The resulting 1270bp long cDNA, named CsMYB1, contained a 933-bp ORF encoding a 310-amino acid protein with a predicted molecular weight of 105.27kDa and a predicted isoelectric point of 4.85 and showed highest homology to plant MYBs likely involved in stress signaling. [Copyright &y& Elsevier]

Abstract: Tea (Camellia sinensis (L.) O. Kuntze) is a commercially important crop that is valued for its secondary metabolites. Light is an important environmental parameter that regulates plant growth and development and influences the phenylpropanoid metabolism in plants. To investigate the molecular mechanism by which light regulates phenylpropanoid metabolism, we established light-induced suppression subtractive hybridization (SSH) cDNA libraries of tea calli. A total of 265 clones from the library were selected, sequenced, and analyzed in this study. Nine diverse ESTs involved in phenylpropanoid biosynthesis were detected in the library. A new CsDFR gene (CsDFR2), higher increment of the expression activated by light than the previously reported CsDFR gene (CsDFR1), was cloned. The key phenylpropanoid compounds and representative genes expression analysis implied that light could be effective for activation of the biosynthesis of phenylpropanoids. Compared to the darkness control, levels of lignins, catechins, and PAs were increased 3.46, 3.00, and 1.21-fold, in light-induced calli, respectively. And lignin biosynthesis genes, involved in CCoAOMT, HCT and CCR, were identified in the light-induced SSH library. Therefore it was assumed that lignins might be the main phenylpropanoid metabolites activated by light in tea calli. In addition, our researches found that catechins, as the main secondary metabolites, significantly decreased in the tea calli compared to those in tea mature leaves, While PAs (polymer of catechins) in calli did not decrease compared to mature leaves. The data suggest that polymerization reaction might be the main pathway of flavonoid metabolism in tea callus. The SSH library established in this study represents a valuable resource for better understanding the mechanisms of light-induced secondary metabolism in tea plants. [Copyright &y& Elsevier]