Transcriptome and Phytochemical Analyses Provide New Insights Into Long Non-Coding RNAs Modulating Characteristic Secondary Metabolites of Oolong Tea (Camellia sinensis) in Solar-Withering

Effect of withering/spreading on the physical and chemical properties of tea: A review

Withering and spreading, though slightly differing in their parameters, share the same aim of moisture reduction in tea leaves, and they have a strong impact on the physical and chemical properties of tea. Even though researchers tend to pay close attention to the characteristic crafts of different teas, increasing investigations begin to focus on the withering process due to its profound effects on the composition and content of quality-related compounds. This review provides an overview of tea withering process to address questions comprehensively during withering. Hence, it is expected in this review to figure out factors that affect withering results, the way withering influences the physical and chemical properties of withered leaves and tea quality, and intelligent technologies and devices targeted at withering processes to promote the modernization of the tea industry. Herein, several key withering parameters, including duration, temperature, humidity, light irradiation, airflow, and more, are tailored to different tea types, demanding further exploration of advanced withering devices and real-time monitoring systems. The development of real-time monitoring technology enables objective and real-time adjustment of withering status in order to optimize withering results. Tea quality, including taste, aroma, and color quality, is first shaped during withering due to the change of composition and content of quality-related metabolites through (non)enzymatic reactions, which are easily influenced by the factors above. A thorough understanding of withering is key to improving tea quality effectively and scientifically.

Evolutionarily conserved 12-oxophytodienoate reductase trans-lncRNA pair affects disease resistance in tea (Camellia sinensis) via the jasmonic acid signaling pathway

Long non-coding RNAs (lncRNAs) have gathered significant attention due to their pivotal role in plant growth, development, and biotic and abiotic stress resistance. Despite this, there is still little understanding regarding the functions of lncRNA in these domains in the tea plant (Camellia sinensis), mainly attributable to the insufficiencies in gene manipulation techniques for tea plants. In this study, we designed a novel strategy to identify evolutionarily conserved trans-lncRNA (ECT-lncRNA) pairs in plants. We used highly consistent base sequences in the exon-overlapping region between trans-lncRNAs and their target gene transcripts. Based on this method, we successfully screened 24 ECT-lncRNA pairs from at least two or more plant species. In tea, as observed in model plants such as Arabidopsis, alfalfa, potatoes, and rice, there exists a trans-lncRNA capable of forming an ECT-lncRNA pair with transcripts of the 12-oxophytodienoate reductase (OPR) family, denoted as the OPRL/OPR pair. Considering evolutionary perspectives, the OPRL gene cluster in each species likely originates from a replication event of the OPR gene cluster. Gene manipulation and gene expression analysis revealed that CsOPRL influences disease resistance by regulating CsOPR expression in tea plants. Furthermore, the knockout of StOPRL1 in Solanum tuberosum led to aberrant growth characteristics and strong resistance to fungal infection. This study provides insights into a strategy for the screening and functional verification of ECT-lncRNA pairs.

Combined multi-omics approach to analyze the flavor characteristics and formation mechanism of gabaron green tea

Gabaron green tea (GAGT) has unique flavor and health benefits through the special anaerobic treatment. However, how this composite processing affects the aroma formation of GAGT and the regulatory mechanism was rarely reported. This study used nontargeted metabolomics and molecular sensory science to overlay screen differential metabolites and key aroma contributors. The potential regulatory mechanism of anaerobic treatment on the aroma formation of GAGT was investigated by transcriptomics and correlation analyses. Five volatiles: benzeneacetaldehyde, nonanal, geraniol, linalool, and linalool oxide III, were screened as target metabolites. Through the transcriptional-level differential genes screening and analysis, some CsERF transcription factors in the ethylene signaling pathway were proposed might participate the response to the anaerobic treatment. They might regulate the expression of related genes in the metabolic pathway of the target metabolites thus affecting the GAGT flavor. The findings of this study provide novel information on the flavor and its formation of GAGT.

Noncoding RNAs in regulation of plant secondary metabolism

Plant secondary metabolites (PSMs) are a large class of structurally diverse molecules, mainly consisting of terpenoids, phenolic compounds, and nitrogen-containing compounds, which play active roles in plant development and stress responses. The biosynthetic processes of PSMs are governed by a sophisticated regulatory network at multiple levels. Noncoding RNAs (ncRNAs) such as microRNAs (miRNAs), long ncRNAs (lncRNAs), and circular RNAs (circRNAs) may serve as post-transcriptional regulators for plant secondary metabolism through acting on genes encoding either transcription factors or participating enzymes in relevant metabolic pathways. High-throughput sequencing technologies have facilitated the large-scale identifications of ncRNAs potentially involved in plant secondary metabolism in model plant species as well as certain species with enriched production of specific types of PSMs. Moreover, a series of miRNA-target modules have been functionally characterized to be responsible for regulating PSM biosynthesis and accumulation in plants under abiotic or biotic stresses. In this review, we will provide an overview of current findings on the ncRNA-mediated regulation of plant secondary metabolism with special attention to its participation in plant stress responses, and discuss possible issues to be addressed in future fundamental research and breeding practice.

Update on functional analysis of long non-coding RNAs in common crops

With the rapid advances in next-generation sequencing technology, numerous non-protein-coding transcripts have been identified, including long noncoding RNAs (lncRNAs), which are functional RNAs comprising more than 200 nucleotides. Although lncRNA-mediated regulatory processes have been extensively investigated in animals, there has been considerably less research on plant lncRNAs. Nevertheless, multiple studies on major crops showed lncRNAs are involved in crucial processes, including growth and development, reproduction, and stress responses. This review summarizes the progress in the research on lncRNA roles in several major crops, presents key strategies for exploring lncRNAs in crops, and discusses current challenges and future prospects. The insights provided in this review will enhance our comprehension of lncRNA functions in crops, with potential implications for improving crop genetics and breeding.

Effects of Monascus purpureus on ripe Pu-erh tea in different fermentation methods and identification of characteristic volatile compounds

The present study aimed to explore the key volatile compounds (VCs) that lead to the formation of characteristic flavors in ripe Pu-erh tea (RIPT) fermented by Monascus purpureus (M. purpureus). Headspace solid-phase microextraction coupled with gas chromatography/mass spectrometry (HS-SPME-GC-MS), orthogonal partial least square-discriminant analysis (OPLS-DA) were employed for a comprehensive analysis of the VCs present in RIPT fermented via different methods and were further identified by odor activity value (OAV). The VCs 1,2-dimethoxybenzene, 1,2,3-trimethoxybenzene, (E)-linalool oxide (pyranoid), methyl salicylate, linalool, β-ionone, β-damascenone were the key characteristic VCs of RIPT fermented by M. purpureus. OAV and Gas chromatography-olfactometry (GC-O) further indicated that β-damascenone was the highest contribution VCs to the characteristic flavor of RIPT fermented by M. purpureus. This study reveals the specificities and contributions of VCs present in RIPT under different fermentation methods, thus providing new insights into the influence of microorganisms on RIPT flavor.

Harnessing Phytohormones: Advancing Plant Growth and Defence Strategies for Sustainable Agriculture

Phytohormones, pivotal regulators of plant growth and development, are increasingly recognized for their multifaceted roles in enhancing crop resilience against environmental stresses. In this review, we provide a comprehensive synthesis of current research on utilizing phytohormones to enhance crop productivity and fortify their defence mechanisms. Initially, we introduce the significance of phytohormones in orchestrating plant growth, followed by their potential utilization in bolstering crop defences against diverse environmental stressors. Our focus then shifts to an in-depth exploration of phytohormones and their pivotal roles in mediating plant defence responses against biotic stressors, particularly insect pests. Furthermore, we highlight the potential impact of phytohormones on agricultural production while underscoring the existing research gaps and limitations hindering their widespread implementation in agricultural practices. Despite the accumulating body of research in this field, the integration of phytohormones into agriculture remains limited. To address this discrepancy, we propose a comprehensive framework for investigating the intricate interplay between phytohormones and sustainable agriculture. This framework advocates for the adoption of novel technologies and methodologies to facilitate the effective deployment of phytohormones in agricultural settings and also emphasizes the need to address existing research limitations through rigorous field studies. By outlining a roadmap for advancing the utilization of phytohormones in agriculture, this review aims to catalyse transformative changes in agricultural practices, fostering sustainability and resilience in agricultural settings.

Integrated transcriptomics and metabolomics analysis provides insights into aromatic volatiles formation in Cinnamomum cassia bark at different harvesting times

BACKGROUND

Cinnamomum cassia Presl, classified in the Lauraceae family, is widely used as a spice, but also in medicine, cosmetics, and food. Aroma is an important factor affecting the medicinal and flavoring properties of C. cassia, and is mainly determined by volatile organic compounds (VOCs); however, little is known about the composition of aromatic VOCs in C. cassia and their potential molecular regulatory mechanisms. Here, integrated transcriptomic and volatile metabolomic analyses were employed to provide insights into the formation regularity of aromatic VOCs in C. cassia bark at five different harvesting times.

RESULTS

The bark thickness and volatile oil content were significantly increased along with the development of the bark. A total of 724 differentially accumulated volatiles (DAVs) were identified in the bark samples, most of which were terpenoids. Venn analysis of the top 100 VOCs in each period showed that twenty-eight aromatic VOCs were significantly accumulated in different harvesting times. The most abundant VOC, cinnamaldehyde, peaked at 120 months after planting (MAP) and dominated the aroma qualities. Five terpenoids, α-copaene, β-bourbonene, α-cubebene, α-funebrene, and δ-cadinene, that peaked at 240 MAP could also be important in creating C. cassia's characteristic aroma. A list of 43,412 differentially expressed genes (DEGs) involved in the biosynthetic pathways of aromatic VOCs were identified, including phenylpropanoids, mevalonic acid (MVA) and methylerythritol phosphate (MEP). A gene-metabolite regulatory network for terpenoid and phenylpropanoid metabolism was constructed to show the key candidate structural genes and transcription factors involved in the biosynthesis of terpenoids and phenylpropanoids.

CONCLUSIONS

The results of our research revealed the composition and changes of aromatic VOCs in C. cassia bark at different harvesting stages, differentiated the characteristic aroma components of cinnamon, and illuminated the molecular mechanism of aroma formation. These foundational results will provide technical guidance for the quality breeding of C. cassia.

Chromatin accessibility mediated transcriptome changes contribute to flavor substance alterations and jasmonic acid hyperaccumulation during oolong tea withering process

During the oolong tea withering process, abiotic stresses induce significant changes in the content of various flavor substances and jasmonic acid (JA). However, the changes in chromatin accessibility during withering and their potential impact remain poorly understood. By integrating ATAC-seq, RNA-seq, metabolite, and hormone assays, we characterized the withering treatment-induced changes in chromatin accessibility, gene expression levels, important metabolite contents, and JA and JA-ILE contents. Additionally, we analyzed the effects of chromatin accessibility alterations on gene expression changes, content changes of important flavor substances, and JA hyperaccumulation. Our analysis identified a total of 3451 open- and 13 426 close-differentially accessible chromatin regions (DACRs) under withering treatment. Our findings indicate that close-DACRs-mediated down-regulated differentially expressed genes (DEGs) resulted in the reduced accumulation of multiple catechins during withering, whereas open-DACRs-mediated up-regulated DEGs contributed to the increased accumulation of important terpenoids, JA, JA-ILE and short-chain C5/C6 volatiles. We further highlighted important DACRs-mediated DEGs associated with the synthesis of catechins, terpenoids, JA and JA and short-chain C5/C6 volatiles and confirmed the broad effect of close-DACRs on catechin synthesis involving almost all enzymes in the pathway during withering. Importantly, we identified a novel MYB transcription factor (CsMYB83) regulating catechin synthesis and verified the binding of CsMYB83 in the promoter-DACRs regions of key catechin synthesis genes using DAP-seq. Overall, our results not only revealed a landscape of chromatin alters-mediated transcription, flavor substance and hormone changes under oolong tea withering, but also provided target genes for flavor improvement breeding in tea plant.

The applications of CRISPR/Cas-mediated microRNA and lncRNA editing in plant biology: shaping the future of plant non-coding RNA research

MAIN CONCLUSION

CRISPR/Cas technology has greatly facilitated plant non-coding RNA (ncRNA) biology research, establishing itself as a promising tool for ncRNA functional characterization and ncRNA-mediated plant improvement. Throughout the last decade, the promising genome editing tool clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated proteins (Cas; CRISPR/Cas) has allowed unprecedented advances in the field of plant functional genomics and crop improvement. Even though CRISPR/Cas-mediated genome editing system has been widely used to elucidate the biological significance of a number of plant protein-coding genes, this technology has been barely applied in the functional analysis of those non-coding RNAs (ncRNAs) that modulate gene expression, such as microRNAs (miRNAs) and long non-coding RNAs (lncRNAs). Nevertheless, compelling findings indicate that CRISPR/Cas-based ncRNA editing has remarkable potential for deciphering the biological roles of ncRNAs in plants, as well as for plant breeding. For instance, it has been demonstrated that CRISPR/Cas tool could overcome the challenges associated with other approaches employed in functional genomic studies (e.g., incomplete knockdown and off-target activity). Thus, in this review article, we discuss the current status and progress of CRISPR/Cas-mediated ncRNA editing in plant science in order to provide novel prospects for further assessment and validation of the biological activities of plant ncRNAs and to enhance the development of ncRNA-centered protocols for crop improvement.

Optimizing Processing Techniques of Oolong Tea Balancing between High Retention of Catechins and Sensory Quality

Catechins are the major flavor substances in teas, which have a variety of health effects; however, high catechin and high sensory quality are a pair of contradictions that are difficult to coordinate. To explore the processing procedure with high catechins and high sensory quality, a single-factor processing experiment was carried out over the processing production of oolong tea. Combined with orthogonal partial least square discriminant analysis (OPLS-DA), correlation analysis, and principal component analysis (PCA), the optimal production procedure for oolong tea is as follows: red light withering for 8 h, leaf rotating for 10 min with a total standing time for 8 h, drum roasting for 5 min at 290 °C, low-temperature rolling (flattening at 4 °C for 5 min, without pressure for 1 min and under pressure for 5 min), microwave drying (800 W for 7.5 min). This study demonstrates a significant increase in the retention of catechins, which contributes to the mellow and brisk tastes of oolong tea, addressing the challenge of catechin content and sensory quality. Our study provides a novel insight into the relationship between the oolong tea processing and flavor formation.

Insights into the roles of long noncoding RNAs in the communication between plants and the environment

In addition to coding proteins, RNA molecules, especially long noncoding RNAs (lncRNAs), have well-established functions in regulating gene expression. The number of studies focused on the roles played by different types of lncRNAs in a variety of plant biological processes has markedly increased. These lncRNA roles involve plant vegetative and reproductive growth and responses to biotic and abiotic stresses. In this review, we examine the classification, mechanisms, and functions of lncRNAs and then emphasize the roles played by these lncRNAs in the communication between plants and the environment mainly with respect to the following environmental factors: temperature, light, water, salt stress, and nutrient deficiencies. We also discuss the consensus among researchers and the remaining challenges and underscore the exciting ways lncRNAs may affect the biology of plants.

Integrated analyses of metabolomics and transcriptomics reveal the potential regulatory roles of long non-coding RNAs in gingerol biosynthesis

BACKGROUND

As the characteristic functional component in ginger, gingerols possess several health-promoting properties. Long non-coding RNAs (lncRNAs) act as crucial regulators of diverse biological processes. However, lncRNAs in ginger are not yet identified so far, and their potential roles in gingerol biosynthesis are still unknown. In this study, metabolomic and transcriptomic analyses were performed in three main ginger cultivars (leshanhuangjiang, tonglingbaijiang, and yujiang 1 hao) in China to understand the potential roles of the specific lncRNAs in gingerol accumulation.

RESULTS

A total of 744 metabolites were monitored by metabolomics analysis, which were divided into eleven categories. Among them, the largest group phenolic acid category contained 143 metabolites, including 21 gingerol derivatives. Of which, three gingerol analogs, [8]-shogaol, [10]-gingerol, and [12]-shogaol, accumulated significantly. Moreover, 16,346 lncRNAs, including 2,513, 1,225, and 2,884 differentially expressed (DE) lncRNA genes (DELs), were identified in all three comparisons by transcriptomic analysis. Gene ontology enrichment (GO) analysis showed that the DELs mainly enriched in the secondary metabolite biosynthetic process, response to plant hormones, and phenol-containing compound metabolic process. Correlation analysis revealed that the expression levels of 11 DE gingerol biosynthesis enzyme genes (GBEGs) and 190 transcription factor genes (TF genes), such as MYB1, ERF100, WRKY40, etc. were strongly correlation coefficient with the contents of the three gingerol analogs. Furthermore, 7 and 111 upstream cis-acting lncRNAs, 1,200 and 2,225 upstream trans-acting lncRNAs corresponding to the GBEGs and TF genes were identified, respectively. Interestingly, 1,184 DELs might function as common upstream regulators to these GBEGs and TFs genes, such as LNC_008452, LNC_006109, LNC_004340, etc. Furthermore, protein-protein interaction networks (PPI) analysis indicated that three TF proteins, MYB4, MYB43, and WRKY70 might interact with four GBEG proteins (PAL1, PAL2, PAL3, and 4CL-4).

CONCLUSION

Based on these findings, we for the first time worldwide proposed a putative regulatory cascade of lncRNAs, TFs genes, and GBEGs involved in controlling of gingerol biosynthesis. These results not only provide novel insights into the lncRNAs involved in gingerol metabolism, but also lay a foundation for future in-depth studies of the related molecular mechanism.

RNA Methylome Reveals the m6A-mediated Regulation of Flavor Metabolites in Tea Leaves under Solar-withering

The epitranscriptomic mark N6-methyladenosine (m6A), which is the predominant internal modification in RNA, is important for plant responses to diverse stresses. Multiple environmental stresses caused by the tea-withering process can greatly influence the accumulation of specialized metabolites and the formation of tea flavor. However, the effects of the m6A-mediated regulatory mechanism on flavor-related metabolic pathways in tea leaves remain relatively uncharacterized. We performed an integrated RNA methylome and transcriptome analysis to explore the m6A-mediated regulatory mechanism and its effects on flavonoid and terpenoid metabolism in tea (Camellia sinensis) leaves under solar-withering conditions. Dynamic changes in global m6A level in tea leaves were mainly controlled by two m6A erasers (CsALKBH4A and CsALKBH4B) during solar-withering treatments. Differentially methylated peak-associated genes following solar-withering treatments with different shading rates were assigned to terpenoid biosynthesis and spliceosome pathways. Further analyses indicated that CsALKBH4-driven RNA demethylation can directly affect the accumulation of volatile terpenoids by mediating the stability and abundance of terpenoid biosynthesis-related transcripts and also indirectly influence the flavonoid, catechin, and theaflavin contents by triggering alternative splicing-mediated regulation. Our findings revealed a novel layer of epitranscriptomic gene regulation in tea flavor-related metabolic pathways and established a link between the m6A-mediated regulatory mechanism and the formation of tea flavor under solar-withering conditions.

Effects of Sun Withering Degree on Black Tea Quality Revealed via Non-Targeted Metabolomics

In this study, the effects of different sun withering degrees (75% (CK), 69% (S69), 66% (S66), 63% (S63), and 60% (S60) water content in the withered leaves) on black tea sensory quality were investigated by means of sensory evaluation plus metabolomics analysis. Sensory evaluation results showed higher sensory quality scores for the black tea in S69-S66, due to better freshness, sweeter taste, and a sweet and even floral and fruity aroma. Additionally, 65 non-volatile components were identified using Ultra Performance Liquid Chromatography-Quadrupole-Time of Flight-Mass Spectrometry (UPLC-Q-TOF/MS). Among them, the content increase of amino acids and theaflavins was found to promote the freshness and sweetness of black tea. The aroma of tea was analyzed using combined Solvent Assisted Flavor Evaporation-Gas Chromatography-Mass Spectrometry (SAFE-GC-MS) and Headspace-Solid Phase Micro Extract-Gas Chromatography-Mass Spectrometry (HS-SPME-GC-MS), and 180 volatiles were identified, including 38 variable importance in projection (VIP) > 1 (p < 0.05) and 25 Odor Activity Value (OAV) > 1 volatiles. Statistical analysis revealed 11 volatiles as potential major aroma differential metabolites in black tea with a different sun withering degree, such as volatile terpenoids (linalool, geraniol, (E)-citral, and β-myrcene), amino-acid-derived volatiles (benzeneethanol, benzeneacetaldehyde, and methyl salicylate), carotenoid-derived volatiles (jasmone and β-damascenone), and fatty-acid-derived volatiles ((Z)-3-hexen-1-ol and (E)-2-hexenal). Among them, volatile terpenoids and amino acid derived volatiles mainly contributed to the floral and fruity aroma quality of sun-withered black tea.

Aroma characteristics of Wuyi rock tea prepared from 16 different tea plant varieties

Wuyi rock tea (WRT) is famous for its long history and unique characteristic of floral, fruity and nutty flavors. This study investigated the aroma characteristics of WRTs prepared from 16 different oolong tea plant varieties. The sensory evaluation results showed that all WRTs had an 'Yan flavor' taste, and the odor was strong and lasting. Roasted, floral and fruity odors were the prime aroma profiles for WRTs. Furthermore, a total of 368 volatile compounds were detected using HS-SPME-GC-MS and analyzed with OPLS-DA and HCA methods. The volatile compounds heterocyclic compounds, esters, hydrocarbons, terpenoids and ketones were the major aromatic components of the WRTs. Specifically, the volatile profiles among newly selected cultivars were comparatively analyzed, and 205 differential volatile compounds were found with variable importance in the projection (VIP) values above 1.0. These results indicated that the aroma profiles of WRTs were mainly dependent on the cultivar specificities of volatile compounds.

The Impact of Different Withering Approaches on the Metabolism of Flavor Compounds in Oolong Tea Leaves

In this study, complementary metabolomic and proteomic analyses were conducted on the solar- and indoor-withered oolong tea leaves, and freshly plucked leaves as the control, for the purpose to reveal the mechanisms underlying the initial formation of some flavor determinants during the early stage of oolong tea processing. As a result, a total of 978 non-volatile compounds and 152 volatile compounds were identified, the flavonoids and several esters were differently accumulated in various tea samples. In total, 7048 proteins were qualitatively and quantitatively determined, the analysis on pathway enrichment showed that phenylpropanoid, flavonoid metabolisms, and protein processing in endoplasmic reticulum were the major pathways discriminating the different tea samples. The joint protein-metabolite analysis showed that the multiple stresses such as dehydration, heat, and ultra-violet irradiation occurred during the withering step induced the dynamic and distinct changes in the biochemical network in the treated leaves compared to fresh leaves. The significant decreases in flavonoids, xanthine alkaloids, and several amino acids contributed to the alleviation of bitter or astringent taste of withered leaves, although the decomposition of L-theanine resulted in the loss of umami flavor over the solar-withering step. Moreover, the fruity or floral aromas, especially volatile terpenoids and phenylpropanoids/benzenoids, were retained or accumulated in the solar withered leaves, potentially aiding the formation of a better characteristic flavor of oolong tea made by indoor withered tea leaves. Distinct effects of solar- and indoor-withering methods on the flavor determinant formation provide a novel insight into the relationship between the metabolite accumulation and flavor formation during the withering step of oolong tea production.

Quantitative Measurement Reveals Dynamic Volatile Changes and Potential Biochemical Mechanisms during Green Tea Spreading Treatment

Quantitative data provide clues for biochemical reactions or regulations. The absolute quantification of volatile compounds in tea is complicated by their low abundance, volatility, thermal liability, matrix complexity, and instrumental sensitivity. Here, by integrating solvent-assisted flavor evaporation extraction with a gas chromatography-triple quadrupole mass spectrometry platform, we successfully established a method based on multiple reaction monitoring (MRM). The method was validated by multiple parameters, including the linear range, limit of detection, limit of quantification, precision, repeatability, stability, and accuracy. This method was then applied to measure temporal changes of endogenous volatiles during green tea spreading treatment. In total, 38 endogenous volatiles were quantitatively measured, which are derived from the shikimic acid pathway, mevalonate pathway, 2-C-methylerythritol-4-phosphate pathway, and fatty acid derivative pathway. Hierarchical clustering and heat-map analysis demonstrated four different changing patterns during green tea spreading treatment. Pathway analysis was then conducted to explore the potential biochemistry underpinning these dynamic change patterns. Our data demonstrated that the established MRM method showed high selectivity and sensitivity for quantitative tea volatile measurement and offered novel insights about volatile formation during green tea spreading.

Effect of red light on the composition of metabolites in tea leaves during the withering process using untargeted metabolomics

BACKGROUND

Red light withering significantly improves the sensory flavor qualities of tea, although changes in metabolites during this process have not been systematically studied until now. The present study comprehensively analyzes metabolites in withered tea leaves at 2-h intervals up to 12 h under red light (630 nm) and dark conditions using ultra performance liquid chromatography-high resolution mass spectrometry (untargeted metabolomics).

RESULTS

Ninety-four non-volatile compounds are identified and relatively quantified, including amino acids, catechins, dimeric catechins, flavonol glycosides, glycosidically-bound volatiles, phenolic acids and nucleosides. The results show that amino acids, catechins and dimeric catechins are most affected by red light treatment. Ten free amino acids, theaflavins and theasinensin A increase after red light irradiation, whereas epigallocatechin gallate and catechin fall.

CONCLUSION

The present study provides a comprehensive and systematic profile of the dynamic effects of red light on withering tea and a rationale for its use in tea processing quality control. © 2021 Society of Chemical Industry.

SMRT and Illumina RNA sequencing reveal the complexity of terpenoid biosynthesis in Zanthoxylum armatum

Sichuan pepper (Zanthoxylum armatum DC) is a popular spice and is often prescribed in traditional Chinese medicine to treat vomiting, diarrhea, ascariasis and eczema, among other conditions. Volatile oils from Z. armatum leaves contain active ingredients, with terpenoids being one of the main components. In the present study, the combination of sequencing data of Z. armatum from PacBio single molecule real time (SMRT) and Illumina RNA sequencing (RNA-Seq) platforms facilitated an understanding of the gene regulatory network of terpenoid biosynthesis in pepper leaves. The leaves of three developmental stages from two Z. armatum cultivars, 'Rongchangwuci' (WC) and 'Zhuye' (ZY), were selected as test materials to construct sequencing libraries. A total of 143,122 predictions of unique coding sequences, 105,465 simple sequence repeats, 20,145 transcription factors and 4719 long non-coding RNAs (lncRNAs) were identified, and 142,829 transcripts were successfully annotated. The occurrence of alternative splicing events was verified by reverse transcription PCR, and quantitative real-time PCR was used to confirm the expression pattern of six randomly selected lncRNAs. A total of 96,931 differentially expressed genes were filtered from different samples. According to functional annotation, a total of 560 candidate genes were involved in terpenoid synthesis, of which 526 were differentially expressed genes (DEGs). To identify the key genes involved in terpenoid biosynthesis, the module genes in different samples, including structural and transcription factors genes, were analyzed using the weighted gene co-expression network method, and the co-expression network of genes was constructed. Thirty-one terpenoids were identified by gas chromatography-mass spectrometry. The correlation between 18 compounds with significantly different contents and genes with high connectivity in the module was jointly analyzed in both cultivars, yielding 12 candidate DEGs presumably involved in the regulation of terpenoid biosynthesis. Our findings showed that full-length transcriptome SMRT and Illumina RNA-Seq can play an important role in studying organisms without reference genomes and elucidating the gene regulation of a biosynthetic pathway.

Perillyl alcohol and quercetin modulate the expression of non-coding RNAs MIAT, H19, miR-29a, and miR-33a in pulmonary artery hypertension in rats

Background

Non-coding RNAs, including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), play critical roles in the pathogenesis and progression of pulmonary artery hypertension (PAH). LncRNA H19, myocardial infarction-associated transcript (MIAT), miR-29a, and miR-33a have been suggested as potential targets for treating arterial hypertension. We explored the expression pattern of non-coding RNAs H19, MIAT, miR-29a, and miR-33a in monocrotaline (MCT)-induced PAH rats. Moreover, we investigated whether perillyl alcohol (PA) and quercetin (QS), two plant derivatives with beneficial effects on PAH-induced abnormalities, act through regulating the expression of these non-coding RNAs.

Methods

Male Wistar rats (n = 30) were divided into five groups. MCT (60 mg/kg) was injected subcutaneously to induce PAH. PA (50 mg/kg daily) and QS (30 mg/kg daily) were administered three weeks after induction of PAH. H&E staining and qRT-PCR were performed to assess arteriole wall thickness and gene expression, respectively.

Results

Right ventricular systolic pressure (RVSP) and right ventricular hypertrophy (RVH) increased in MCT and MCT + Veh. groups compared to the control group (in both P < 0.001). QS and PA decreased RVSP and RVH significantly. Wall thickness and fibrosis score in the MCT group (score 3) increased compared to the control group (score 0). PA and QS ameliorated wall thickness and fibrosis to score 1 (mild). Also, the expression of miR-29a and miR-33a decreased in the PAH group (in both, P < 0.001). Treatment with PA and QS decreased the expression of H19 (P < 0.001) and MIAT (P < 0.01) and increased the expression of miR-29a (P < 0.01) and miR-33a significantly (P < 0.05 for QS and P < 0.001 for PA).

Conclusions

The beneficial effects of PA and QS on PAH-induced abnormalities were exerted through returning the dysregulated expression of H19, MIAT, miR-29a, and miR-33a to normal levels in rats with MTC-induced PAH. This study emphasized the therapeutic potential of PA and QS in PAH. However, more detailed investigations are needed to clarify the underlying molecular mechanisms.

Development and Validation of a Prognostic Signature Associated With Tumor Microenvironment Based on Autophagy-Related lncRNA Analysis in Hepatocellular Carcinoma

Objective: The present study aimed to establish a prognostic signature based on the autophagy-related long non-coding RNAs (lncRNAs) analysis in patients with hepatocellular carcinoma (HCC).

Methods: Patients with HCC from The Cancer Genome Atlas (TCGA) were taken as the training cohort, and patients from the International Cancer Genome Consortium (ICGC) were treated as the validation cohort. Autophagy-related lncRNAs were obtained via a co-expression network analysis. According to univariate and multivariate analyses, a multigene prognostic signature was constructed in the training cohort. The predictive power of the signature was confirmed in both cohorts. The detailed functions were investigated using functional analysis. The single-sample gene set enrichment analysis (ssGSEA) score was used to evaluate the tumor microenvironment. The expression levels of immunotherapy and targeted therapy targets between the two risk groups were compared. Finally, a nomogram was constructed by integrating clinicopathological parameters with independently predictive value and the risk score.

Results: Four autophagy-related lncRNAs were identified to establish a prognostic signature, which separated patients into high- and low-risk groups. Survival analysis showed that patients in the high-risk group had a shorter survival time in both cohorts. A time-independent receiver-operating characteristic (ROC) curve and principal component analysis (PCA) confirmed that the prognostic signature had a robust predictive power and reliability in both cohorts. Functional analysis indicated that the expressed genes in the high-risk group are mainly enriched in autophagy- and cancer-related pathways. ssGSEA revealed that the different risk groups were associated with the tumor microenvironment. Moreover, the different risk groups had positive correlations with the expressions of specific mutant genes. Multivariate analysis showed that the risk score also exhibited excellent predictive power irrespective of clinicopathological characteristics in both cohorts. A nomogram was established. The nomogram showed good discrimination, with Harrell's concordance index (C-index) of 0.739 and good calibration.

Conclusion: The four autophagy-related lncRNAs could be used as biological biomarkers and therapeutic targets. The prognostic signature and nomogram might aid clinicians in individual treatment optimization and clinical decision-making for patients with HCC.

Metabolomics Provides A Novel Interpretation of the Changes in Main Compounds during Black Tea Processing through Different Drying Methods

This study aimed to compare the effect of hot roller (HR) drying and hot air (HA) drying on the sensory evaluation, chemical quality, antioxidant activity, and metabolic profile of Yihong Congou black tea processed from E’cha NO1. The Yihong Congou black tea dried with HA obtained higher sensory scores and better chemical qualities such as the hue of tea brew color (a and b), content of theaflavins, thearubigins, water extract, free amino acids, tea polyphenol, and the ratio of polyphenol to amino acids as well as higher antioxidant capacities compared to that dried with HR. The HA drying tea increased the contents of volatile compounds that had positive correlation with sweet and flowery flavor, while the HR drying tea increased the contents of volatile compounds related to fruity flavor. Moreover, non-targeted metabolomics data indicated that the levels of most free amino acids significantly increased, while the levels of most soluble sugars reduced in the HA drying method compared to the HR drying method. The metabolic analysis was also consistent with the above results and revealed that D-ribose and gallic acid were the main characteristic metabolites of HA drying. Our results could provide a technical reference and theoretical guide to processing a high quality of Yihong Congou black tea.

From "Dark Matter" to "Star": Insight Into the Regulation Mechanisms of Plant Functional Long Non-Coding RNAs

Long non-coding RNAs (lncRNAs) play a vital role in a variety of biological functions in plant growth and development. In this study, we provided an overview of the molecular mechanisms of lncRNAs in interacting with other biomolecules with an emphasis on those lncRNAs validated only by low-throughput experiments. LncRNAs function through playing multiple roles, including sponger for sequestering RNA or DNA, guider or decoy for recruiting or hijacking transcription factors or peptides, and scaffold for binding with chromatin modification complexes, as well as precursor of microRNAs or small interfering RNAs. These regulatory roles have been validated in several plant species with a comprehensive list of 73 lncRNA-molecule interaction pairs in 16 plant species found so far, suggesting their commonality in the plant kingdom. Such initial findings of a small number of functional plant lncRNAs represent the beginning of what is to come as lncRNAs with unknown functions were found in orders of magnitude more than proteins.

Identification and characterization of long non-coding RNA and their response against citrus bark cracking viroid infection in Humulus lupulus

Long non-coding RNAs (lncRNAs) are a highly heterogeneous class of non-protein-encoding transcripts that play an essential regulatory role in diverse biological processes, including stress responses. The severe stunting disease caused by Citrus bark cracking viroid (CBCVd) poses a major threat to the production of Humulus lupulus (hop) plants. In this study, we systematically investigate the characteristics of the lncRNAs in hop and their role in CBCVd-infection using RNA-sequencing data. Following a stringent filtration criterion, a total of 3598 putative lncRNAs were identified with a high degree of certainty, of which 19% (684) of the lncRNAs were significantly differentially expressed (DE) in CBCVd-infected hop, which were predicted to be mainly involved in plant-pathogen interactions, kinase cascades, secondary metabolism and phytohormone signal transduction. Besides, several lncRNAs and CBCVd-responsive lncRNAs were identified as the precursor of microRNAs and predicted as endogenous target mimics (eTMs) for hop microRNAs involved in CBCVd-infection.

Interplay between miRNAs and lncRNAs: Mode of action and biological roles in plant development and stress adaptation

Plants employ sophisticated mechanisms to control developmental processes and to cope with environmental changes at transcriptional and post-transcriptional levels. MicroRNAs (miRNAs) and long noncoding RNAs (lncRNAs), two classes of endogenous noncoding RNAs, are key regulators of gene expression in plants. Recent studies have identified the interplay between miRNAs and lncRNAs as a novel regulatory layer of gene expression in plants. On one hand, miRNAs target lncRNAs for the production of phased small interfering RNAs (phasiRNAs). On the other hand, lncRNAs serve as origin of miRNAs or regulate the accumulation or activity of miRNAs at transcription and post-transcriptional levels. Theses lncRNA-miRNA interplays are crucial for plant development, physiology and responses to biotic and abiotic stresses. In this review, we summarize recent advances in the biological roles, interaction mechanisms and computational predication methods of the interplay between miRNAs and lncRNAs in plants.

Dynamic characteristics and functional analysis provide new insights into long non-coding RNA responsive to Verticillium dahliae infection in Gossypium hirsutum

BACKGROUND

Verticillium wilt is a widespread and destructive disease, which causes serious loss of cotton yield and quality. Long non-coding RNA (lncRNA) is involved in many biological processes, such as plant disease resistance response, through a variety of regulatory mechanisms, but their possible roles in cotton against Verticillium dahliae infection remain largely unclear.

RESULTS

Here, we measured the transcriptome of resistant G. hirsutum following infection by V. dahliae and 4277 differentially expressed lncRNAs (delncRNAs) were identified. Localization and abundance analysis revealed that delncRNAs were biased distribution on chromosomes. We explored the dynamic characteristics of disease resistance related lncRNAs in chromosome distribution, induced expression profiles, biological function, and these lncRNAs were divided into three categories according to their induced expression profiles. For the delncRNAs, 687 cis-acting pairs and 14,600 trans-acting pairs of lncRNA-mRNA were identified, which indicated that trans-acting was the main way of Verticillium wilt resistance-associated lncRNAs regulating target mRNAs in cotton. Analyzing the regulation pattern of delncRNAs revealed that cis-acting and trans-acting lncRNAs had different ways to influence target genes. Gene Ontology (GO) enrichment analysis revealed that the regulatory function of delncRNAs participated significantly in stimulus response process, kinase activity and plasma membrane components. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis indicated that delncRNAs participated in some important disease resistance pathways, such as plant-pathogen interaction, alpha-linolenic acid metabolism and plant hormone signal transduction. Additionally, 21 delncRNAs and 10 target genes were identified as being involved in alpha-linolenic acid metabolism associated with the biosynthesis of jasmonic acid (JA). Subsequently, we found that GhlncLOX3 might regulate resistance to V. dahliae through modulating the expression of GhLOX3 implicated in JA biosynthesis. Further functional analysis showed that GhlncLOX3-silenced seedlings displayed a reduced resistance to V. dahliae, with down-regulated expression of GhLOX3 and decreased content of JA.

CONCLUSION

This study shows the dynamic characteristics of delncRNAs in multiaspect, and suggests that GhlncLOX3-GhLOX3-JA network participates in response to V. dahliae invasion. Our results provide novel insights for genetic improvement of Verticillium wilt resistance in cotton using lncRNAs.

Genome-Wide Investigation of N6-Methyladenosine Regulatory Genes and Their Roles in Tea (Camellia sinensis) Leaves During Withering Process

N6-methyladenosine (m6A), one of the internal modifications of RNA molecules, can directly influence RNA abundance and function without altering the nucleotide sequence, and plays a pivotal role in response to diverse environmental stresses. The precise m6A regulatory mechanism comprises three types of components, namely, m6A writers, erasers, and readers. To date, the research focusing on m6A regulatory genes in plant kingdom is still in its infancy. Here, a total of 34 m6A regulatory genes were identified from the chromosome-scale genome of tea plants. The expansion of m6A regulatory genes was driven mainly by whole-genome duplication (WGD) and segmental duplication, and the duplicated gene pairs evolved through purifying selection. Gene structure analysis revealed that the sequence variation contributed to the functional diversification of m6A regulatory genes. Expression pattern analysis showed that most m6A regulatory genes were differentially expressed under environmental stresses and tea-withering stage. These observations indicated that m6A regulatory genes play essential roles in response to environmental stresses and tea-withering stage. We also found that RNA methylation and DNA methylation formed a negative feedback by interacting with each other's methylation regulatory genes. This study provided a foundation for understanding the m6A-mediated regulatory mechanism in tea plants under environmental stresses and tea-withering stage.

Integrated Transcriptome, microRNA, and Phytochemical Analyses Reveal Roles of Phytohormone Signal Transduction and ABC Transporters in Flavor Formation of Oolong Tea (Camellia sinensis) during Solar Withering

The unique aroma and flavor of oolong tea develop during the withering stage of postharvest processing. We explored the roles of miRNA-related regulatory networks during tea withering and their effects on oolong tea quality. We conducted transcriptome and miRNA analyses to identify differentially expressed (DE) miRNAs and target genes among fresh leaves, indoor-withered leaves, and solar-withered leaves. We identified 32 DE-miRNAs and 41 target genes involved in phytohormone signal transduction and ABC transporters. Further analyses indicated that these two pathways regulated the accumulation of flavor-related metabolites during tea withering. Flavonoid accumulation was correlated with the miR167d_1-ARF-GH3, miR845-ABCC1-3/ABCC2, miR166d-5p_1-ABCC1-2, and miR319c_3-PIF-ARF modules. Terpenoid content was correlated with the miR171b-3p_2-DELLA-MYC2 and miR166d-5p_1-ABCG2-MYC2 modules. These modules inhibited flavonoid biosynthesis and enhanced terpenoid biosynthesis in solar-withered leaves. Low auxin and gibberellic acid contents and circRNA-related regulatory networks also regulated the accumulation of flavor compounds in solar-withered leaves. Our analyses reveal how solar withering produces high-quality oolong tea.

UV-B Induces Distinct Transcriptional Re-programing in UVR8-Signal Transduction, Flavonoid, and Terpenoids Pathways in Camellia sinensis

Plants are known to respond to Ultraviolet-B radiation (UV-B: 280-320 nm) by generating phenolic metabolites which absorbs UV-B light. Phenolics are extraordinarily abundant in Camellia sinensis leaves and are considered, together with pleasant volatile terpenoids, as primary flavor determinants in tea beverages. In this study, we focused on the effects of UV-B exposure (at 35 μW cm^-2 for 0, 0.5, 2, and 8 h) on tea transcriptional and metabolic alterations, specifically related to tea flavor metabolite production. Out of 34,737 unigenes, a total of 18,081 differentially expressed genes (DEGs) due to UV-B treatments were identified. Additionally, the phenylpropanoid pathway was found as one of the most significantly UV-B affected top 20 KEGG pathways while flavonoid and monoterpenoid pathway-related genes were enhanced at 0.5 h. In the UVR8-signal transduction pathway, UVR8 was suppressed at both short and long exposure of UV-B with genes downstream differentially expressed. Divergent expression of MYB4 at different treatments could have differentially altered structural and regulatory genes upstream of flavonoid biosynthesis pathways. Suppression of MYB4-1&3 at 0.5 h could have led to the up-regulation of structural CCOAOMT-1&2, HST-1&2, DFR-4, ANR-2, and LAR-1&3 genes resulting in accumulation of specialized metabolites at a shorter duration of UV-B exposure. Specialized metabolite profiling revealed the correlated alterations in the abundances of catechins and some volatile terpenoids in all the treatments with significant accumulation of specialized metabolites at 0.5 h treatment. A significant increase in specialized metabolites at 0.5 h treatment and no significant alteration observed at longer UVB treatment suggested that shorter exposure to UV-B led to different display in gene expression and accumulation of specialized metabolites in tea shoots in response to UV-B stress. Taken together, our results indicated that the UV-B treatment applied in this study differentially altered the UVR8-signal transduction, flavonoid and terpenoid pathways at transcriptional and metabolic levels in tea plants. Our results show strong potential for UV-B application in flavor improvement in tea at the industrial level.