Transcriptomic Analysis of Tea Plant Responding to Drought Stress and Recovery

The Receptor Kinases DRUS1 and DRUS2 Behave Distinctly in Osmotic Stress Tolerance by Modulating the Root System Architecture via Auxin Signaling

Receptor kinases DRUS1 (Dwarf and Runtish Spikelet1) and DRUS2 are orthologues of the renowned Arabidopsis thaliana gene FERONIA, which play redundant roles in rice growth and development. Whether the two duplicated genes perform distinct functions in response to environmental stress is largely unknown. Here, we found that osmotic stress (OS) and ABA increased DRUS1 expression while decreasing DRUS2. When subjected to osmotic stress, the increased DRUS1 in drus2 mutants suppresses the OsIAA repressors, resulting in a robust root system with an increased number of adventitious and lateral roots as well as elongated primary, adventitious, and lateral roots, conferring OS tolerance. In contrast, the decreased DRUS2 in drus1-1 mutants are not sufficient to suppress OsIAA repressors, leading to a feeble root system with fewer adventitious and lateral roots and hindering seminal root growth, rendering OS intolerance. All these findings offer valuable insights into the biological significance of the duplication of two homologous genes in rice, wherein, if one is impaired, the other one is able to continue auxin-signaling-mediated root growth and development to favor resilience to environmental stress, such as water shortage.

Analyzing the Diversity of MYB Family Response Strategies to Drought Stress in Different Flax Varieties Based on Transcriptome Data

The MYB transcription factor family has numerous members, and is involved in biological activities, such as ABA signaling, which plays an important role in a plant's resistance to abiotic stresses such as drought. However, the diversity of MYB members that respond to drought stress and their regulatory mechanisms in different flax varieties were unclear. In this study, we obtained 855.69 Gb of clean data from 120 flax root samples from 20 flax (Linum usitatissimum L.) varieties, assembled 92,861 transcripts, and identified 434 MYB family members in each variety. The expression profiles of the MYB transcription factor family from 20 flax varieties under drought stress were analyzed. The results indicated that there are four strategies by which the MYB family responds to drought stress in these 20 flax varieties, each of which has its own specific processes, such as development, reproduction, and localization processes. The four strategies also include common biological processes, such as stimulus responses, metabolic processes, and biological regulation. The WGCNA method was subsequently employed to identify key members of the MYB family involved in response strategies to drought stress. The results demonstrated that a 1R-MYB subfamily gene co-expression network is significantly related to the gibberellin response and cytokinin-activated signaling pathway processes in the 'Strategy 4' for MYB family response to drought, identifying core genes such as Lus.scaffold70.240. Our results showed a diversity of MYB family responses to drought stress within flax varieties, and these results contribute to deciphering the mechanisms of the MYB family regulation of drought resistance. This will promote the more accurate breeding development of flax to adapt to agricultural production under drought conditions.

Multilayer omics landscape analyses reveal the regulatory responses of tea plants to drought stress

Adverse environments, especially drought conditions, deeply influence plant development and growth in all aspects, and the yield and quality of tea plants are largely dependent on favorable growth conditions. Although tea plant responses to drought stress (DS) have been studied, a comprehensive multilayer epigenetic, transcriptomic, and proteomic investigation of how tea responds to DS is lacking. In this study, we generated DNA methylome, transcriptome, proteome, and phosphoproteome data to explore multiple regulatory landscapes in the tea plant response to DS. An integrated multiomics analysis revealed the response of tea plants to DS at multiple regulatory levels. Furthermore, a set of DS-responsive genes involved in photosynthesis, transmembrane transportation, phytohormone metabolism and signaling, secondary metabolite pathways, transcription factors, protein kinases, posttranslational and epigenetic modification, and other key stress-responsive genes were identified for further functional investigation. These results reveal the multilayer regulatory landscape of the tea plant response to DS and provide insight into the mechanisms of these DS responses.

Phytohormone Response of Drought-Acclimated Illicium difengpi (Schisandraceae)

Illicium difengpi (Schisandraceae), which is an endemic, medicinal, and endangered species found in small and isolated populations that inhabit karst mountain areas, has evolved strategies to adapt to arid environments and is thus an excellent material for exploring the mechanisms of tolerance to severe drought. In experiment I, I. difengpi plants were subjected to three soil watering treatments (CK, well-watered treatment at 50% of the dry soil weight for 18 days; DS, drought stress treatment at 10% of the dry soil weight for 18 days; DS-R, drought-rehydration treatment at 10% of the dry soil weight for 15 days followed by rewatering to 50% of the dry soil weight for another 3 days). The effects of the drought and rehydration treatments on leaf succulence, phytohormones, and phytohormonal signal transduction in I. difengpi plants were investigated. In experiment II, exogenous abscisic acid (ABA, 60 mg L-1) and zeatin riboside (ZR, 60 mg L-1) were sprayed onto DS-treated plants to verify the roles of exogenous phytohormones in alleviating drought injury. Leaf succulence showed marked changes in response to the DS and DS-R treatments. The relative concentrations of ABA, methyl jasmonate (MeJA), salicylic acid glucoside (SAG), and cis-zeatin riboside (cZR) were highly correlated with relative leaf succulence. The leaf succulence of drought-treated I. difengpi plants recovered to that observed with the CK treatment after exogenous application of ABA or ZR. Differentially expressed genes involved in biosynthesis and signal transduction of phytohormones (ABA and JA) in response to drought stress were identified by transcriptomic profiling. The current study suggested that the phytohormones ABA, JA, and ZR may play important roles in the response to severe drought and provides a preliminary understanding of the physiological mechanisms involved in phytohormonal regulation in I. difengpi, an endemic, medicinal, and highly drought-tolerant plant found in extremely small populations in the karst region of South China.

Two galactinol synthases contribute to the drought response of Camellia sinensis

MAIN CONCLUSION

CsGolS2-1 and CsGolS2-2 are involved in the transcriptional mechanism and play an important role in the drought response of tea plants. GolS is critical for the biosynthesis of galactinol and has been suggested to contribute to drought tolerance in various plants. However, whether GolS plays a role in drought response and the underlying transcriptional mechanism of GolS genes in response to drought stress in tea plants is still unclear. In this study, we found that drought stress promotes the accumulation of galactinol in tea leaves and that the expression of CsGolS2-1 and CsGolS2-2, which encode proteins capable of catalyzing galactinol biosynthesis, is continuously and dramatically induced by drought stress. Moreover, transgenic Arabidopsis plants expressing CsGolS2-1 and CsGolS2-2 were more drought-tolerant than WT plants, as evidenced by increased cell membrane stability. In addition, the drought-responsive transcription factor CsWRKY2 has been shown to positively regulate the expression of CsGolS2-1 and CsGolS2-2 by directly binding to their promoters. Furthermore, CsVQ9 was found to interact with CsWRKY2 and promote its transcriptional function to activate CsGolS2-1 and CsGolS2-2 expression. Taken together, our findings provide insights not only into the positive role played by CsGolS2-1 and CsGolS2-2 in the drought response of tea plants but also into the transcriptional mechanisms involved.

Comprehensive analysis of the laccase gene family in tea plant highlights its roles in development and stress responses

BACKGROUND

Laccase (LAC) is the pivotal enzyme responsible for the polymerization of monolignols and stress responses in plants. However, the roles of LAC genes in plant development and tolerance to diverse stresses are still largely unknown, especially in tea plant (Camellia sinensis), one of the most economically important crops worldwide.

RESULTS

In total, 51 CsLAC genes were identified, they were unevenly distributed on different chromosomes and classified into six groups based on phylogenetic analysis. The CsLAC gene family had diverse intron-exon patterns and a highly conserved motif distribution. Cis-acting elements in the promoter demonstrated that promoter regions of CsLACs encode various elements associated with light, phytohormones, development and stresses. Collinearity analysis identified some orthologous gene pairs in C. sinensis and many paralogous gene pairs among C. sinensis, Arabidopsis and Populus. Tissue-specific expression profiles revealed that the majority of CsLACs had high expression in roots and stems and some members had specific expression patterns in other tissues, and the expression patterns of six genes by qRT‒PCR were highly consistent with the transcriptome data. Most CsLACs showed significant variation in their expression level under abiotic (cold and drought) and biotic (insect and fungus) stresses via transcriptome data. Among them, CsLAC3 was localized in the plasma membrane and its expression level increased significantly at 13 d under gray blight treatment. We found that 12 CsLACs were predicted to be targets of cs-miR397a, and most CsLACs showed opposite expression patterns compared to cs-miR397a under gray blight infection. Additionally, 18 highly polymorphic SSR markers were developed, these markers can be widely used for diverse genetic studies of tea plants.

CONCLUSIONS

This study provides a comprehensive understanding of the classification, evolution, structure, tissue-specific profiles, and (a)biotic stress responses of CsLAC genes. It also provides valuable genetic resources for functional characterization towards enhancing tea plant tolerance to multiple (a)biotic stresses.

Transcriptome-based variations effectively untangling the intraspecific relationships and selection signals in Xinyang Maojian tea population

As one of the world's top three popular non-alcoholic beverages, tea is economically and culturally valuable. Xinyang Maojian, this elegant green tea, is one of the top ten famous tea in China and has gained prominence for thousands of years. However, the cultivation history of Xinyang Maojian tea population and selection signals of differentiation from the other major variety Camellia sinensis var. assamica (CSA) remain unclear. We newly generated 94 Camellia sinensis (C. sinensis) transcriptomes including 59 samples in the Xinyang area and 35 samples collected from 13 other major tea planting provinces in China. Comparing the very low resolution of phylogeny inferred from 1785 low-copy nuclear genes with 94 C. sinensis samples, we successfully resolved the phylogeny of C. sinensis samples by 99,115 high-quality SNPs from the coding region. The sources of tea planted in the Xinyang area were extensive and complex. Specifically, Shihe District and Gushi County were the two earliest tea planting areas in Xinyang, reflecting a long history of tea planting. Furthermore, we identified numerous selection sweeps during the differentiation of CSA and CSS and these positive selection genes are involved in many aspects such as regulation of secondary metabolites synthesis, amino acid metabolism, photosynthesis, etc. Numerous specific selective sweeps of modern cultivars were annotated with functions in various different aspects, indicating the CSS and CSA populations possibly underwent independent specific domestication processes. Our study indicated that transcriptome-based SNP-calling is an efficient and cost-effective method in untangling intraspecific phylogenetic relationships. This study provides a significant understanding of the cultivation history of the famous Chinese tea Xinyang Maojian and unravels the genetic basis of physiological and ecological differences between the two major tea subspecies.

Combined analysis of transcriptome and metabolome reveals the molecular mechanism and candidate genes of Haloxylon drought tolerance

Haloxylon ammodendron and Haloxylon persicum, as typical desert plants, show strong drought tolerance and environmental adaptability. They are ideal model plants for studying the molecular mechanisms of drought tolerance. Transcriptomic and metabolomic analyses were performed to reveal the response mechanisms of H. ammodendron and H. persicum to a drought environment at the levels of transcription and physiological metabolism. The results showed that the morphological structures of H. ammodendron and H. persicum showed adaptability to drought stress. Under drought conditions, the peroxidase activity, abscisic acid content, auxin content, and gibberellin content of H. ammodendron increased, while the contents of proline and malondialdehyde decreased. The amino acid content of H. persicum was increased, while the contents of proline, malondialdehyde, auxin, and gibberellin were decreased. Under drought conditions, 12,233 and 17,953 differentially expressed genes (DEGs) were identified in H. ammodendron and H. persicum , respectively, including members of multiple transcription factor families such as FAR1, AP2/ERF, C2H2, bHLH, MYB, C2C2, and WRKY that were significantly up-regulated under drought stress. In the positive ion mode, 296 and 452 differential metabolites (DEMs) were identified in H. ammodendron and H. persicum, respectively; in the negative ion mode, 252 and 354 DEMs were identified, primarily in carbohydrate and lipid metabolism. A combined transcriptome and metabolome analysis showed that drought stress promoted the glycolysis/gluconeogenesis pathways of H. ammodendron and H. persicum and increased the expression of amino acid synthesis pathways, consistent with the physiological results. In addition, transcriptome and metabolome were jointly used to analyze the expression changes of the genes/metabolites of H. ammodendron and H. persicum that were associated with drought tolerance but were regulated differently in the two plants. This study identified drought-tolerance genes and metabolites in H. ammodendron and H. persicum and has provided new ideas for studying the drought stress response of Haloxylon.

United States tea: A synopsis of ongoing tea research and solutions to United States tea production issues

Tea is a steeped beverage made from the leaves of Camellia sinensis. Globally, this healthy, caffeine-containing drink is one of the most widely consumed beverages. At least 50 countries produce tea and most of the production information and tea research is derived from international sources. Here, we discuss information related to tea production, genetics, and chemistry as well as production issues that affect or are likely to affect emerging tea production and research in the United States. With this review, we relay current knowledge on tea production, threats to tea production, and solutions to production problems to inform this emerging market in the United States.

Genome-wide identification and expression analysis of the calmodulin-binding transcription activator (CAMTA) family genes in tea plant

Background

As a type of calmodulin binding protein, CAMTAs are widely involved in vegetative and reproductive processes as well as various hormonal and stress responses in plants. To study the functions of CAMTA genes in tea plants, we investigated bioinformatics analysis and performed qRT-PCR analysis of the CAMTA gene family by using the genomes of ‘ShuChaZao’ tea plant cultivar.

Results

In this study, 6 CsCAMTAs were identified from tea plant genome. Bioinformatics analysis results showed that all CsCAMTAs contained six highly conserved functional domains. Tissue-specific analysis results found that CsCAMTAs played great roles in mediating tea plant aging and flowering periods. Under hormone and abiotic stress conditions, most CsCAMTAs were upregulated at different time points under different treatment conditions. In addition, the expression levels of CsCAMTA1/3/4/6 were higher in cold-resistant cultivar ‘LongJing43’ than in the cold-susceptible cultivar ‘DaMianBai’ at cold acclimation stage, while CsCAMTA2/5 showed higher expression levels in ‘DaMianBai’ than in ‘LongJing43’ during entire cold acclimation periods.

Conclusions

In brief, the present results revealed that CsCAMTAs played great roles in tea plant growth, development and stress responses, which laid the foundation for deeply exploring their molecular regulation mechanisms.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08894-x.

Dynamic changes in metabolic and lipidomic profiles of tea plants during drought stress and re-watering

Tea (Camellia sinensis L.), as an evergreen plant, needs a humid environment. Water deficit would diminish tea yield and quality. We analyzed the dynamic changes in the metabolite and lipid profiling of tea leaves under various drought conditions and re-watering to determine the metabolic changes in tea leaves responding to drought challenges. In all, 119 metabolites showed substantial alterations in drought-stressed tea plants, including sugars and sugar alcohols, amino acids, and tricarboxylic acid cycle intermediates and lipids. We detected 29 lipids and they were classified into phosphatidylglycerol (PG), phosphatidic acid (PA), sulfoquinovosyl-diacylglycerol (SQDG), phosphatidylcholine (PC), lyso-phosphatidylcholine (LysoPC), and phosphatidylinositol (PI). The levels of sugar, sugar alcohol, and sugar precursors may change as a response to drought stress. Compared with these metabolites, the membrane lipids showed more dynamic changes in tea under drought stresses. Furthermore, metabolic recovery was only partial, with the majority of the examined metabolites exhibiting significantly different levels between samples from re-watered and well-watered tea plants. The findings also showed that comprehensive metabolomic and lipidomic approaches were efficient in elucidating the impacts of drought stress on tea plant metabolism. Our findings are valuable for understanding the mechanisms behind drought tolerance in tea plants from the metabolism perspective and utilizing the compounds to improve the drought tolerance of tea plants.

Effects of exogenous calcium on the drought response of the tea plant (Camellia sinensis (L.) Kuntze)

Background

Drought is one of the major factors reducing the yield of many crops worldwide, including the tea crop (Camellia sinensis (L.) Kuntze). Calcium participates in most of cellular signaling processes, and its important role in stress detection and triggering a response has been shown in many crops. The aim of this study was to evaluate possible effects of calcium on the tea plant response to drought.

Methods

Experiments were conducted using 3-year-old potted tea plants of the best local cultivar Kolkhida. Application of ammonium nitrate (control treatment) or calcium nitrate (Ca treatment) to the soil was performed before drought induction. Next, a 7-day drought was induced in both groups of plants. The following physiological parameters were measured: relative electrical conductivity, pH of cell sap, and concentrations of cations, sugars, and amino acids. In addition, relative expression levels of 40 stress-related and crop quality-related genes were analyzed.

Results

Under drought stress, leaf electrolyte leakage differed significantly, indicating greater damage to cell membranes in control plants than in Ca-treated plants. Calcium application resulted in greater pH of cell sap; higher accumulation of tyrosine, methionine, and valine; and a greater Mg²⁺ content as compared to control plants. Drought stress downregulated most of the quality-related genes in both groups of tea plants. By contrast, significant upregulation of some genes was observed, namely CRK45, NAC26, TPS11, LOX1, LOX6, Hydrolase22, DREB26, SWEET2, GS, ADC, DHN2, GOLS1, GOLS3, and RHL41. Among them, three genes (LOX1, RHL41, and GOLS1) showed 2-3 times greater expression in Ca-treated plants than in control plants. Based on these results, it can be speculated that calcium affects galactinol biosynthesis and participates in the regulation of stomatal aperture not only through activation of abscisic-acid signaling but also through jasmonic-acid pathway activation. These findings clarify calcium-mediated mechanisms of drought defense in tree crops. Thus, calcium improves the drought response in the tea tree.

Genome-Wide Identification and Expression Analysis of Isopentenyl transferase Family Genes during Development and Resistance to Abiotic Stresses in Tea Plant (Camellia sinensis)

The tea plant is an important economic crop and is widely cultivated. Isopentenyl transferase (IPT) is the first and rate-limiting enzyme of cytokinin (CK) signaling, which plays key roles in plant development and abiotic stress. However, the IPT gene family in tea plants has not been systematically investigated until now. The phylogenetic analyses, gene structures, and conserved domains were predicted here. The results showed that a total of 13 CsIPT members were identified from a tea plant genome database and phylogenetically classified into four groups. Furthermore, 10 CsIPT members belonged to plant ADP/ATP-IPT genes, and 3 CsIPTs were tRNA-IPT genes. There is a conserved putative ATP/GTP-binding site (P-loop motif) in all the CsIPT sequences. Based on publicly available transcriptome data as well as through RNA-seq and qRT-PCR analysis, the CsIPT genes which play key roles in the development of different tissues were identified, respectively. Furthermore, CsIPT6.2 may be involved in the response to different light treatments. CsIPT6.4 may play a key role during the dormancy and flush of the lateral buds. CsIPT5.1 may play important regulatory roles during the development of the lateral bud, leaf, and flower. CsIPT5.2 and CsIPT6.2 may both play key roles for increased resistance to cold-stress, whereas CsIPT3.2 may play a key role in improving resistance to high-temperature stress as well as drought-stress and rewatering. This study could provide a reference for further studies of CsIPT family’s functions and could contribute to tea molecular breeding.

Integrated transcriptomic and gibberellin analyses reveal genes related to branch development in Eucalyptus urophylla

Tree branches affect the planting density and basal scab, which act as important attributes in the yield and quality of trees. Eucalyptus urophylla is an important pioneer tree with characteristics of strong adaptability, fast growth, short rotation period, and low disease and pest pressures. In this study, we collected ZQUC14 and LDUD26 clones and compared their transcriptomes and metabolomes from mature xylem, phloem, and developing tissues to identify factors that may influence branch development. In total, 32,809 differentially expressed genes (DEGs) and 18 gibberellin (GA) hormones were detected in the five sampled tissues. Searches of the kyoto Encyclopedia of Genes and Genomes pathways identified mainly genes related to diterpenoid biosynthesis, plant MAPK signaling pathways, plant hormone signal transduction, glycerolipid metabolism, peroxisome, phenylpropanoid biosynthesis, ABC transporters, and brassinosteroid biosynthesis. Furthermore, gene expression trend analysis and weighted gene co-expression network analysis revealed 13 genes likely involved in diterpenoid biosynthesis, including five members of the 2OG-Fe(II) oxygenase superfamily, four cytochrome P450 genes, and four novel genes. In GA signal transduction pathways, 24 DEGs were found to positively regulate branch formation. These results provide a comprehensive analysis of branch development based on the transcriptome and metabolome, and help clarify the molecular mechanisms of E. urophylla.

Transcriptome Profiling to the Effects of Drought Stress on Different Propagation Modes of Tea Plant (Camellia sinensis)

Tea plant (Camellia sinensis) is an important economic beverage crop. Drought stress seriously affects the growth and development of tea plant and the accumulation of metabolites, as well as the production, processing, yield and quality of tea. Therefore, it is necessary to understand the reaction mechanism of tea plant under drought conditions and find efficient control methods. Based on transcriptome sequencing technology, this study studied the difference of metabolic level between sexual and asexual tea plants under drought stress. In this study, there were multiple levels of up-regulation and down-regulation of differential genes related to cell composition, molecular function and biological processes. Transcriptomic data show that the metabolism of tea plants with different propagation modes of QC and ZZ is different under drought conditions. In the expression difference statistics, it can be seen that the differential genes of QC are significantly more than ZZ; GO enrichment analysis also found that although differential genes in biological process are mainly enriched in the three pathways of metabolic, single organism process and cellular process, cellular component is mainly enriched in cell, cell part, membrane, and molecular function, and binding, catalytic activity, and transporter activity; the enrichment order of differential genes in these pathways is different in QC and ZZ. This difference is caused by the way of reproduction. The further study of these differential genes will lay a foundation for the cultivation methods and biotechnology breeding to improve the quality of tea.

Camellia sinensis small GTPase gene (CsRAC1) involves in response to salt stress, drought stress and ABA signaling pathway

RAC/ROP gene (RACs) is a plant-specific small GTPases. RACs play an irreplaceable role in the tissue dynamics of cytoskeleton, vesicle transport and hormone signal transmission in plants. In the present study, a novel gene from RACs family, CsRAC1, was identified from tea [Camellia sinensis (L.) O. Kuntze]. CsRAC1 contained a 591-bp open reading frame and encoded a putative protein of 197 amino acids. Subcellular localization analysis in leaves of transgenic tobacco and root tips of Arabidopsis thaliana showed that CsRAC1 targeted the nucleus and cell membrane. The expression of CsRAC1 induced by abiotic stresses such as cold, heat, drought, salt and abscisic acid has also been verified by RT-qPCR. Further verification of biological function of CsRAC1 showed that overexpression of CsRAC1 increased the sensitivity of A. thaliana to salt stress, improved the tolerance of mature A. thaliana to drought stress, and enhanced the inhibition of ABA on seed germination of A. thaliana. In addition, the antioxidant system regulated by CsRAC1 mainly worked in mature A. thaliana. The results indicate that CsRAC1 is involved in the response of C. sinensis to salt, drought stress and ABA signaling pathway.

Research progress on the response of tea catechins to drought stress

Drought stress (DS) is the most important abiotic stress affecting yield and quality of tea worldwide. DS causes oxidative stress to cells due to the accumulation of reactive oxygen species (ROS). As non-enzymatic antioxidants, tea catechins can scavenge excess ROS in response to DS. Further, catechin accumulation contributes to the formation of oxidative polymerization products (e.g. theaflavins and thearubigins) that improve the quality of black tea. However, there are no systematic reports on the response of tea catechins to DS. First, we reviewed the available literature on the response of tea plants to DS. Second, we summarized the current knowledge of ROS production in tea leaves under DS and typical antioxidant response mechanisms. Third, we conducted a detailed review of the changes in catechin levels in tea under different drought conditions. We found that the total amounts of catechin and o-quinone increased under DS conditions. We propose that the possible mechanisms underlying tea catechin accumulation under DS conditions include (i) autotrophic formation of o-quinone, (ii) polymerization of proanthocyanidins that directly scavenge excess ROS, and (iii) formation of metal ion complexes and by influencing the antioxidant systems that indirectly eliminate excess ROS. Finally, we discuss ways of potentially improving black tea quality using drought before picking in the summer/fall dry season. In summary, we mainly discuss the antioxidant mechanisms of tea catechins under DS and the possibility of using drought to improve black tea quality. Our review provides a theoretical basis for the production of high-quality black tea under DS conditions. © 2021 Society of Chemical Industry.

Time-course transcriptomic analysis of Petunia ×hybrida leaves under water deficit stress using RNA sequencing

Water deficit limits plant growth and development, resulting in quality loss of horticultural crops. However, there is limited information on gene regulation and signaling pathways related to water deficit stress response at multiple time points. The objective of this research was to investigate global gene expression patterns under water deficit stress to provide an insight into how petunia (Petunia ×hybrida 'Mitchell Diploid') responded in the process of stress. Nine-week-old petunias were irrigated daily or placed under water stress by withholding water. Stressed plants reduced stomatal conductance after five days of water deficit, indicating they perceived stress and initiated stress response mechanisms. To analyze transcriptomic changes at the early stage of water deficit, leaf tissue samples were collected 1, 3, and 5 days after water was withheld for RNA sequencing. Under water deficit stress, 154, 3611, and 980 genes were upregulated and 41, 2806, and 253 genes were downregulated on day 1, 3, and 5, respectively. Gene Ontology analysis revealed that redox homeostasis processes through sulfur and glutathione metabolism pathways, and hormone signal transduction, especially abscisic acid and ethylene, were enriched under water deficit stress. Thirty-four transcription factor families were identified, including members of AP2/ERF, NAC, MYB-related, C2H2, and bZIP families, and TFs in AP2/ERF family was the most abundant in petunia. Interestingly, only one member of GRFs was upregulated on day 1, while most of TFs were differentially expressed on day 3 and/or 5. The transcriptome data from this research will provide valuable molecular resources for understanding the early stages of water stress-responsive networks as well as engineering petunia with enhanced water stress tolerance.

Comparative Expression Analysis of Stress-Inducible Candidate Genes in Response to Cold and Drought in Tea Plant [Camellia sinensis (L.) Kuntze]

Cold and drought are two of the most severe threats affecting the growth and productivity of the tea plant, limiting its global spread. Both stresses cause osmotic changes in the cells of the tea plant by decreasing their water potential. To develop cultivars that are tolerant to both stresses, it is essential to understand the genetic responses of tea plant to these two stresses, particularly in terms of the genes involved. In this study, we combined literature data with interspecific transcriptomic analyses (using Arabidopsis thaliana and Solanum lycopersicum) to choose genes related to cold tolerance. We identified 45 stress-inducible candidate genes associated with cold and drought responses in tea plants based on a comprehensive homologous detection method. Of these, nine were newly characterized by us, and 36 had previously been reported. The gene network analysis revealed upregulated expression in ICE1-related cluster of bHLH factors, HSP70/BAM5 connected genes (hexokinases, galactinol synthases, SnRK complex, etc.) indicating their possible co-expression. Using qRT-PCR we revealed that 10 genes were significantly upregulated in response to both cold and drought in tea plant: HSP70, GST, SUS1, DHN1, BMY5, bHLH102, GR-RBP3, ICE1, GOLS1, and GOLS3. SnRK1.2, HXK1/2, bHLH7/43/79/93 were specifically upregulated in cold, while RHL41, CAU1, Hydrolase22 were specifically upregulated in drought. Interestingly, the expression of CIP was higher in the recovery stage of both stresses, indicating its potentially important role in plant recovery after stress. In addition, some genes, such as DHN3, bHLH79, PEI54, SnRK1.2, SnRK1.3, and Hydrolase22, were significantly positively correlated between the cold and drought responses. CBF1, GOLS1, HXK2, and HXK3, by contrast, showed significantly negative correlations between the cold and drought responses. Our results provide valuable information and robust candidate genes for future functional analyses intended to improve the stress tolerance of the tea plant and other species.

Biochemical and Genetic Responses of Tea (Camellia sinensis (L.) Kuntze) Microplants under Mannitol-Induced Osmotic Stress In Vitro

Osmotic stress is a major factor reducing the growth and yield of many horticultural crops worldwide. To reveal reliable markers of tolerant genotypes, we need a comprehensive understanding of the responsive mechanisms in crops. In vitro stress induction can be an efficient tool to study the mechanisms of responses in plants to help gain a better understanding of the physiological and genetic responses of plant tissues against each stress factor. In the present study, the osmotic stress was induced by addition of mannitol into the culture media to reveal biochemical and genetic responses of tea microplants. The contents of proline, threonine, epigallocatechin, and epigallocatechin gallate were increased in leaves during mannitol treatment. The expression level of several genes, namely DHN2, LOX1, LOX6, BAM, SUS1, TPS11, RS1, RS2, and SnRK1.3, was elevated by 2–10 times under mannitol-induced osmotic stress, while the expression of many other stress-related genes was not changed significantly. Surprisingly, down-regulation of the following genes, viz. bHLH12, bHLH7, bHLH21, bHLH43, CBF1, WRKY2, SWEET1, SWEET2, SWEET3, INV5, and LOX7, was observed. During this study, two major groups of highly correlated genes were observed. The first group included seven genes, namely CBF1, DHN3, HXK2,SnRK1.1, SPS, SWEET3, and SWEET1. The second group comprised eight genes, viz. DHN2, SnRK1.3, HXK3, RS1, RS2,LOX6, SUS4, and BAM5. A high level of correlation indicates the high strength connection of the genes which can be co-expressed or can be linked to the joint regulons. The present study demonstrates that tea plants develop several adaptations to cope under osmotic stress in vitro; however, some important stress-related genes were silent or downregulated in microplants.

Exogenous abscisic acid induces the lipid and flavonoid metabolism of tea plants under drought stress

Abscisic acid (ABA) is an important phytohormone responsible for activating drought resistance, but the regulation mechanism of exogenous ABA on tea plants under drought stress was rarely reported. Here, we analyzed the effects of exogenous ABA on genes and metabolites of tea leaves under drought stress using transcriptomic and metabolomic analysis. The results showed that the exogenous ABA significantly induced the metabolic pathways of tea leaves under drought stress, including energy metabolism, amino acid metabolism, lipid metabolism and flavonoids biosynthesis. In which, the exogenous ABA could clearly affect the expression of genes involved in lipid metabolism and flavonoid biosynthesis. Meanwhile, it also increased the contents of flavone, anthocyanins, flavonol, isoflavone of tea leaves under drought stress, including, kaempferitrin, sakuranetin, kaempferol, and decreased the contents of glycerophospholipids, glycerolipids and fatty acids of tea leaves under drought stress. The results suggested that the exogenous ABA could alleviate the damages of tea leaves under drought stress through inducing the expression of the genes and altering the contents of metabolites in response to drought stress. This study will be helpful to understand the mechanism of resilience to abiotic stress in tea plant and provide novel insights into enhancing drought tolerance in the future.

Molecular bases of responses to abiotic stress in trees

Trees are constantly exposed to climate fluctuations, which vary with both time and geographic location. Environmental changes that are outside of the physiological favorable range usually negatively affect plant performance and trigger responses to abiotic stress. Long-living trees in particular have evolved a wide spectrum of molecular mechanisms to coordinate growth and development under stressful conditions, thus minimizing fitness costs. The ongoing development of techniques directed at quantifying abiotic stress has significantly increased our knowledge of physiological responses in woody plants. However, it is only within recent years that advances in next-generation sequencing and biochemical approaches have enabled us to begin to understand the complexity of the molecular systems that underlie these responses. Here, we review recent progress in our understanding of the molecular bases of drought and temperature stresses in trees, with a focus on functional, transcriptomic, epigenetic, and population genomic studies. In addition, we highlight topics that will contribute to progress in our understanding of the plastic and adaptive responses of woody plants to drought and temperature in a context of global climate change.

Genome-wide characterization of tea plant (Camellia sinensis) Hsf transcription factor family and role of CsHsfA2 in heat tolerance

BACKGROUND

Heat stress factors (Hsfs) play vital roles in signal transduction pathways operating in responses to environmental stresses. However, Hsf gene family has not been thoroughly explored in tea plant (Camellia sinensis L.).

RESULTS

In this study, we identified 25 CsHsf genes in C. sinensis that were separated by phylogenetic analysis into three sub-families (i.e., A, B, and C). Gene structures, conserved domains and motifs analyses indicated that the CsHsf members in each class were relatively conserved. Various cis-acting elements involved in plant growth regulation, hormone responses, stress responses, and light responses were located in the promoter regions of CsHsfs. Furthermore, degradome sequencing analysis revealed that 7 CsHsfs could be targeted by 9 miRNAs. The expression pattern of each CsHsf gene was significantly different in eight tissues. Many CsHsfs were differentially regulated by drought, salt, and heat stresses, as well as exogenous abscisic acid (ABA) and Ca²⁺. In addition, CsHsfA2 was located in the nucleus. Heterologous expression of CsHsfA2 improved thermotolerance in transgenic yeast, suggesting its potential role in the regulation of heat stress response.

CONCLUSIONS

A comprehensive genome-wide analysis of Hsf in C. sinensis present the global identification and functional prediction of CsHsfs. Most of them were implicated in a complex gene regulatory network controlling various abiotic stress responses and signal transduction pathways in tea plants. Additionally, heterologous expression of CsHsfA2 increased thermotolerance of transgenic yeast. These findings provide new insights into the functional divergence of CsHsfs and a basis for further research on CsHsfs functions.

Metabolomics Response for Drought Stress Tolerance in Chinese Wheat Genotypes (Triticum aestivum)

Metabolomics is an effective biotechnological tool that can be used to attain comprehensive information on metabolites. In this study, the profiles of metabolites produced by wheat seedlings in response to drought stress were investigated using an untargeted approach with ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) to determine various physiological processes related to drought tolerance from the cross between drought-tolerant genotype (HX10) and drought-sensitive genotype (YN211). The current study results showed that under drought stress, HX10 exhibited higher growth indices than YN211. After drought stress treatment, a series of phenolics accumulated higher in HX10 than in YN211, whereas the amount of thymine, a pyrimidine, is almost 13 folds of that in YN211. These metabolites, as well as high levels of different amino acids, alkaloids, organic acids, and flavonoids in the drought treated HX10 could help to explain its strong drought-tolerant capacity. The current study explored the understanding of the mechanisms involved in the drought response of wheat seedling; these metabolome data could also be used for potential QTL or GWAS studies to identify locus (loci) or gene(s) associated with these metabolic traits for the crop improvement.

Alternative splicing in tea plants was extensively triggered by drought, heat and their combined stresses

Drought and heat stresses can influence the expressions of genes, and thereby affect the growth and development of plants. Alternative splicing (AS) of genes plays crucial roles through increasing transcriptome diversity in plant stress responses. Tea plants, widely cultivated in the tropics and subtropics, are often simultaneously exposed to drought and heat stresses. In the present study, we performed a global transcriptome of tea leaves treated with drought, heat or their combination. In total, 19,019, 20,025 and 20,253 genes underwent AS in response to drought (DT), heat (HT) and their combined stress (HD), respectively, of which 12,178, 11,912 and 14,413 genes differentially spliced in response to DT, HT and HD, respectively. Also, 2,447 specific differentially spliced genes (DSGs) were found only in response to HD. All DSGs accounted for  48% of the annotated genes in tea tree genome. Comparison of DSGs and differentially expressive genes (DEGs) showed that the proportions of HT and HD-induced DSGs were 13.4% and 9.2%, while the proportion of DT increased to 28.1%. Moreover, the DEG-DSG overlapped genes tended to be enriched in a wide large of pathways in response to DT. The results indicated that the AS of genes in tea leaves was extensively triggered by drought, heat and their combined stresses. In addition, the AS enhanced the transcriptome adaption in response to drought and heat stresses, and the AS also provoked specific molecular functions in response to drought and heat synergy stress. The study might have practical significance for molecular genetic breeding of tea plants with stress resistance.

Development of a DNA-based real-time PCR assay for the quantification of Colletotrichum camelliae growth in tea (Camellia sinensis)

BACKGROUND

Tea, which is produced from new shoots of existing tea plants (Camellia sinensis), is one of the most popular, non-alcoholic, healthy beverages worldwide. Colletotrichum camelliae is one of the dominant fungal pathogens of tea. The interaction of C. camelliae with tea could be a useful pathosystem to elucidate various aspects of woody, medicinal plant-fungal interactions. Currently, many studies characterizing resistance or virulence and aggressiveness use lesion size at the infection sites on the leaves to quantify the growth of the pathogen. However, this method does not offer the sensitivity needed for the robust quantification of small changes in aggressiveness or the accurate quantification of pathogen growth at the early stages of infection.

RESULTS

A quantitative real-time polymerase chain reaction (qRT-PCR) assay was developed for the quantification of C. camelliae growth on tea plant. This method was based on the comparison of fungal DNA in relation to plant biomass. This assay was used to investigate the phenotypes of tea plant cultivars in response to C. camelliae infection. Two cultivars, Zhongcha 108 (ZC108) and Longjing 43 (LJ43), were tested with this method. ZC108 was previously reported as an anthracnose-resistant cultivar against C. camelliae, while LJ43 was susceptible. The traditional lesion measurement method showed that both cultivars were susceptible to a virulent strain of C. camelliae, while the qRT-PCR approach indicated that very little fungal growth occurred in the anthracnose-resistant cultivar ZC108. The observed results in this study were consistent with previously published research. In addition, the DNA-based real-time PCR method was applied for analysis of pathogenic differences in general C. camelliae isolates and among several Colletotrichum spp that infect tea.

CONCLUSIONS

This study showed that the DNA-based qRT-PCR technique is rapid, highly sensitive and easily applicable for routine experiments and could be used in screening for resistant tea plant cultivars or to identify differences in pathogen aggressiveness within and among Colletotrichum species.

Tea plant genomics: achievements, challenges and perspectives

Tea is among the world's most widely consumed non-alcoholic beverages and possesses enormous economic, health, and cultural values. It is produced from the cured leaves of tea plants, which are important evergreen crops globally cultivated in over 50 countries. Along with recent innovations and advances in biotechnologies, great progress in tea plant genomics and genetics has been achieved, which has facilitated our understanding of the molecular mechanisms of tea quality and the evolution of the tea plant genome. In this review, we briefly summarize the achievements of the past two decades, which primarily include diverse genome and transcriptome sequencing projects, gene discovery and regulation studies, investigation of the epigenetics and noncoding RNAs, origin and domestication, phylogenetics and germplasm utilization of tea plant as well as newly developed tools/platforms. We also present perspectives and possible challenges for future functional genomic studies that will contribute to the acceleration of breeding programs in tea plants.

Transcriptome Profiling, Biochemical and Physiological Analyses Provide New Insights towards Drought Tolerance in Nicotiana tabacum L

Drought stress is one of the main factors limiting crop production, which provokes a number of changes in plants at physiological, anatomical, biochemical and molecular level. To unravel the various mechanisms underpinning tobacco (Nicotiana tabacum L.) drought stress tolerance, we conducted a comprehensive physiological, anatomical, biochemical and transcriptome analyses of three tobacco cultivars (i.e., HongHuaDaJinYuan (H), NC55 (N) and Yun Yan-100 (Y)) seedlings that had been exposed to drought stress. As a result, H maintained higher growth in term of less reduction in plant fresh weight, dry weight and chlorophyll content as compared with N and Y. Anatomical studies unveiled that drought stress had little effect on H by maintaining proper leaf anatomy while there were significant changes in the leaf anatomy of N and Y. Similarly, H among the three varieties was the least affected variety under drought stress, with more proline content accumulation and a powerful antioxidant defense system, which mitigates the negative impacts of reactive oxygen species. The transcriptomic analysis showed that the differential genes expression between HongHuaDaJinYuan, NC55 and Yun Yan-100 were enriched in the functions of plant hormone signal transduction, starch and sucrose metabolism, and arginine and proline metabolism. Compared to N and Y, the differentially expressed genes of H displayed enhanced expression in the corresponding pathways under drought stress. Together, our findings offer insights that H was more tolerant than the other two varieties, as evidenced at physiological, biochemical, anatomical and molecular level. These findings can help us to enhance our understanding of the molecular mechanisms through the networks of various metabolic pathways mediating drought stress adaptation in tobacco.

Duplication and transcriptional divergence of three Kunitz protease inhibitor genes that modulate insect and pathogen defenses in tea plant (Camellia sinensis)

Kunitz protease inhibitors (KPIs) are ubiquitous in plants and act as crucial compounds in defense responses against insect attack and pathogen infection. However, the influence of gene duplication on the postdivergence of the CsKPI genes involved in biotic stresses in tea plant is not well known. Here, we identified three CsKPI genes from tea plant (Camellia sinensis) and characterized their expression and evolutionary patterns among plant species. We found that CsKPI1, CsKPI2, and CsKPI3 diverged from their common ancestor 72.94 million years ago (MYA), and the tandem duplication of CsKPI2 and CsKPI3 occurred 26.78 MYA. An in vitro protein assay showed that the three CsKPI proteins were functional and inhibited the production of p-nitroanilide (PNA) from an artificial substrate. The three CsKPI-GFP fusion proteins localized to the cytoplasm. We showed that salicylic acid (SA) and transcripts of CsKPI2 and CsKPI3 significantly accumulated after infection with Glomerella cingulata. The application of exogenous SA stimulated the high expression of both CsKPI2 and CsKPI3 by activating cis-elements within their promoters. Under Ectropis oblique attack, CsKPI1 expression and jasmonic acid (JA) levels were more abundant in both insect-damaged leaf tissues and undamaged neighboring leaves. The application of jasmonic acid methyl ester elicited high expression levels of CsKPI1, suggesting that CsKPI1 accumulation requires JA production in tea plant. The overall findings suggest that the transcriptional divergence of KPI genes after duplication led to the specialized role of CsKPI1 in the physiological response to insect stress; the functional conservation between CsKPI2 and CsKPI3 confers resistance to pathogen infection in tea plant.

Optimized sequencing depth and de novo assembler for deeply reconstructing the transcriptome of the tea plant, an economically important plant species

Background

Tea is the oldest and among the world’s most popular non-alcoholic beverages, which has important economic, health and cultural values. Tea is commonly produced from the leaves of tea plants (Camellia sinensis), which belong to the genus Camellia of family Theaceae. In the last decade, many studies have generated the transcriptomes of tea plants at different developmental stages or under abiotic and/or biotic stresses to investigate the genetic basis of secondary metabolites that determine tea quality. However, these results exhibited large differences, particularly in the total number of reconstructed transcripts and the quality of the assembled transcriptomes. These differences largely result from limited knowledge regarding the optimized sequencing depth and assembler for transcriptome assembly of structurally complex plant species genomes.

Results

We employed different amounts of RNA-sequencing data, ranging from 4 to 84 Gb, to assemble the tea plant transcriptome using five well-known and representative transcript assemblers. Although the total number of assembled transcripts increased with increasing sequencing data, the proportion of unassembled transcripts became saturated as revealed by plant BUSCO datasets. Among the five representative assemblers, the Bridger package shows the best performance in both assembly completeness and accuracy as evaluated by the BUSCO datasets and genome alignment. In addition, we showed that Bridger and BinPacker harbored the shortest runtimes followed by SOAPdenovo and Trans-ABySS.

Conclusions

The present study compares the performance of five representative transcript assemblers and investigates the key factors that affect the assembly quality of the transcriptome of the tea plants. This study will be of significance in helping the tea research community obtain better sequencing and assembly of tea plant transcriptomes under conditions of interest and may thus help to answer major biological questions currently facing the tea industry.

Comparative transcriptomic analysis of high- and low-oil Camellia oleifera reveals a coordinated mechanism for the regulation of upstream and downstream multigenes for high oleic acid accumulation

Tea oil camellia (Camellia oleifera) is an important woody oil tree in southern China. However, little is known regarding the molecular mechanisms that contribute to high oleic acid accumulation in tea oil camellia. Herein, we measured the oil content and fatty acid compositions of high- and low-oil tea oil camellia seeds and investigated the global gene expression profiles by RNA-seq. The results showed that at the early, second and third seed developmental stages, a total of 64, 253, and 124 genes, respectively, were significantly differentially expressed between the high- and low-oil cultivars. Gene ontology (GO) enrichment analysis of the identified differentially expressed transcription factors (TFs; ABI3, FUS3, LEC1, WRI1, TTG2 and DOF4.6) revealed some critical GO terms associated with oil biosynthesis and fatty acid accumulation, including glycolysis, zinc ion binding, positive regulation of fatty acid biosynthetic process, triglyceride biosynthetic process, seed coat development, abscisic acid-mediated signaling pathway and embryo development. Comprehensive comparisons of transcriptomic profiles and expression analysis of multigenes based on qRT-PCR showed that coordinated high expression of the upstream genes HAD, EAR and KASI directly increased the relative levels of C16:0-ACP, which provided enough precursor resources for oleic acid biosynthesis. Continuous high expression of the SAD gene accelerated oleic acid synthesis and accumulation, and coordinated low expression of the downstream genes FAD2, FAD3, FAD7, FAD8 and FAE1 decreased the consumption of oleic acid for conversion. The coordinated regulation of these multigenes ensures the high accumulation of oleic acid in the seeds of tea oil camellia. Our data represent a comprehensive transcriptomic study of high- and low-oil tea oil camellia, not only increasing the number of sequences associated with lipid biosynthesis and fatty acid accumulation in public resource databases but also providing a scientific basis for genetic improvement of the oleic acid content in woody oil trees.

Isolation and Characterization of CsWRKY7, a Subgroup IId WRKY Transcription Factor from Camellia sinensis, Linked to Development in Arabidopsis

WRKY transcription factors (TFs) containing one or two WRKY domains are a class of plant TFs that respond to diverse abiotic stresses and are associated with developmental processes. However, little has been known about the function of WRKY gene in tea plant. In this study, a subgroup IId WRKY gene CsWRKY7 was isolated from Camellia sinensis, which displayed amino acid sequence homology with Arabidopsis AtWRKY7 and AtWRKY15. Subcellular localization prediction indicated that CsWRKY7 localized to nucleus. Cis-acting elements detected in the promotor region of CsWRKY7 are mainly involved in plant response to environmental stress and growth. Consistently, expression analysis showed that CsWRKY7 transcripts responded to NaCl, mannitol, PEG, and diverse hormones treatments. Additionally, CsWRKY7 exhibited a higher accumulation both in old leaves and roots compared to bud. Seed germination and root growth assay indicated that overexpressed CsWRKY7 in transgenic Arabidopsis was not sensitive to NaCl, mannitol, PEG, and low concentration of ABA treatments. CsWRKY7 overexpressing Arabidopsis showed a late-flowering phenotype under normal conditions compared to wild type. Furthermore, gene expression analysis showed that the transcription levels of the flowering time integrator gene FLOWERING LOCUS T (FT) and the floral meristem identity genes APETALA1 (AP1) and LEAFY (LFY) were lower in WRKY7-OE than in the WT. Taken together, these findings indicate that CsWRKY7 TF may participate in plant growth. This study provides a potential strategy to breed late-blooming tea cultivar.

Transcriptional profiling of contrasting genotypes revealed key candidates and nucleotide variations for drought dissection in Camellia sinensis (L.) O. Kuntze

Tea is popular health beverage consumed by millions of people worldwide. Drought is among the acute abiotic stress severely affecting tea cultivation, globally. In current study, transcriptome sequencing of four diverse tea genotypes with inherent contrasting genetic response to drought (tolerant & sensitive) generated more than 140 million reads. De novo and reference-based assembly and functional annotation of 67,093 transcripts with multifarious public protein databases yielded 54,484 (78.2%) transcripts with significant enrichment of GO and KEGG drought responsive pathways in tolerant genotypes. Comparative DGE and qRT analysis revealed key role of ABA dependent & independent pathways, potassium & ABC membrane transporters (AtABCG22, AtABCG11, AtABCC5 & AtABCC4) and antioxidant defence system against oxidative stress in tolerant genotypes, while seems to be failed in sensitive genotypes. Additionally, highly expressed UPL3HECT E3 ligases and RING E3 ligases possibly enhance drought tolerance by actively regulating functional modification of stress related genes. Further, ascertainment of, 80803 high quality putative SNPs with functional validation of key non-synonymous SNPs suggested their implications for developing high-throughput genotyping platform in tea. Futuristically, functionally relevant genomic resources can be potentially utilized for gene discovery, genetic engineering and marker-assisted genetic improvement for better yield and quality in tea under drought conditions.

Transcriptome profiling of the fertile parent and sterile hybrid in tea plant flower buds

Background

The tea plant is a crucial economic crop. The floral organ development consumes a large amount of nutrients, which affects the leaf yield. To understand the mechanism by which the tea plant produces sterile floral buds, we obtained a sterile tea plant by artificial hybridization. RNA-sequencing based transcriptome analysis was implemented in three samples to determine the differentially expressed genes (DEGs) related to flower development.

Results

In this study, a total of 1991 DEGs were identified; 1057 genes were up-regulated and 934 genes were down-regulated in sterile hybrid floral buds. These were mainly distributed in the regulation of biological and metabolic processes. Significantly, auxin biosynthesis genes YUCCA, AUX1 and PIN were dramatically down-regulated, and ARF gene was up-regulated in the sterile hybrid floral buds, and flower development-related genes AP1, AP2 and SPL were changed. A total of 12 energy transfer-related genes were significantly decreased. Furthermore, the expression of 11 transcription factor genes was significantly different.

Conclusion

The transcriptome analysis suggested that the production of sterile floral buds is a complex bioprocess, and that low auxin-related gene levels result in the formation of sterile floral buds in the tea plant.

Global Ubiquitome Profiling Revealed the Roles of Ubiquitinated Proteins in Metabolic Pathways of Tea Leaves in Responding to Drought Stress

Drought stress often affects the expression of genes and proteins in tea plants. However, the global profiling of ubiquitinated (Kub) proteins in tea plants remains unearthed. Here, we performed the ubiquitome in tea leaves under drought stress using antibody-based affinity enrichment coupled with LC-MS/MS analysis. In total, 1,409 lysine Kub sites in 781 proteins were identified, of which 14 sites in 12 proteins were up-regulated and 123 sites in 91 proteins down-regulated under drought stress. The identified Kub proteins were mainly located in the cytosol (31%), chloroplast (27%) and nuclear (19%). Moreover, 5 conserved motifs in EK^ub, EXXXK^ub, K^ubD, K^ubE and K^ubA were extracted. Several Kub sites in ubiquitin-mediated proteolysis-related proteins, including RGLG2, UBC36, UEV1D, RPN10 and PSMC2, might affect protein degradation and DNA repair. Plenty of Kub proteins related to catechins biosynthesis, including PAL, CHS, CHI and F3H, were positively correlated with each other due to their co-expression and co-localization. Furthermore, some Kub proteins involved in carbohydrate and amino acid metabolism, including FBPase, FBA and GAD1, might promote sucrose, fructose and GABA accumulation in tea leaves under drought stress. Our study preliminarily revealed the global profiling of Kub proteins in metabolic pathways and provided an important resource for further study on the functions of Kub proteins in tea plants.

Comparative transcriptome analysis to elucidate the enhanced thermotolerance of tea plants (Camellia sinensis) treated with exogenous calcium

The molecular mechanisms regulating calcium-mediated thermotolerance in Camellia sinensis were revealed by RNA-Sequencing. Heat stress is one of the most remarkable abiotic factors limiting the growth and productivity of Camellia sinensis plants. Calcium helps regulate plant responses to various adverse environmental conditions, including heat stress. In this study, the effects of exogenous calcium on the physiological characteristics of heat-stressed C. sinensis were investigated. A calcium pretreatment increased the proline, soluble sugar, Ca²⁺, and chlorophyll contents, but decreased the malondialdehyde content and relative electrical conductivity in C. sinensis leaves under heat stress. Further analysis of the ultra-structure of chloroplasts indicated that heat stress induced accumulation of starch granules and destruction of the stroma lamella in C. sinensis. However, calcium pretreatment counteracted the adverse effects of heat stress on the structure of the photosynthetic apparatus. These results imply that the calcium pretreatment increased C. sinensis thermotolerance. Moreover, RNA-sequencing was applied to characterize the calcium-mediated transcript-level responses to heat stress. A total of 923 differentially expressed genes (DEGs) including 299 up-regulated and 624 down-regulated genes were identified. Functional annotations indicated that these DEGs were primarily related to signal transduction, transcriptional regulation, and post-translational modification. In addition, a C. sinensis gene [CsCML45 (GenBank: KY652927)] encoding a calmodulin-like protein was isolated. The heterologous expression of CsCML45 enhanced the thermotolerance of transgenic Arabidopsis thaliana plants. These results may be useful for characterizing the calcium-mediated molecular mechanism responsible for C. sinensis thermotolerance.

Functional annotation of putative QTL associated with black tea quality and drought tolerance traits

The understanding of black tea quality and percent relative water content (%RWC) traits in tea (Camellia sinensis) by a quantitative trait loci (QTL) approach can be useful in elucidation and identification of candidate genes underlying the QTL which has remained to be difficult. The objective of the study was to identify putative QTL controlling black tea quality and percent relative water traits in two tea populations and their F1 progeny. A total of 1,421 DArTseq markers derived from the linkage map identified 53 DArTseq markers to be linked to black tea quality and %RWC. All 53 DArTseq markers with unique best hits were identified in the tea genome. A total of 5,592 unigenes were assigned gene ontology (GO) terms, 56% comprised biological processes, cellular component (29%) and molecular functions (15%), respectively. A total of 84 unigenes in 15 LGs were assigned to 25 different Kyoto Encyclopedia of Genes and Genomes (KEGG) database pathways based on categories of secondary metabolite biosynthesis. The three major enzymes identified were transferases (38.9%), hydrolases (29%) and oxidoreductases (18.3%). The putative candidate proteins identified were involved in flavonoid biosynthesis, alkaloid biosynthesis, ATPase family proteins related to abiotic/biotic stress response. The functional annotation of putative QTL identified in this current study will shed more light on the proteins associated with caffeine and catechins biosynthesis and % RWC. This study may help breeders in selection of parents with desirable DArTseq markers for development of new tea cultivars with desirable traits.

Transcriptomic signature reveals mechanism of flower bud distortion in witches'-broom disease of soybean (Glycine max)

BACKGROUND

Soybean (Glycine max L. Merril) crop is major source of edible oil and protein for human and animals besides its various industrial uses including biofuels. Phytoplasma induced floral bud distortion syndrome (FBD), also known as witches' broom syndrome (WBS) has been one of the major biotic stresses adversely affecting its productivity. Transcriptomic approach can be used for knowledge discovery of this disease manifestation by morpho-physiological key pathways.

RESULTS

We report transcriptomic study using Illumina HiSeq NGS data of FBD in soybean, revealing 17,454 differentially expressed genes, 5561 transcription factors, 139 pathways and 176,029 genic region putative markers single sequence repeats, single nucleotide polymorphism and Insertion Deletion. Roles of PmbA, Zn-dependent protease, SAP family and auxin responsive system are described revealing mechanism of flower bud distortion having abnormalities in pollen, stigma development. Validation of 10 randomly selected genes was done by qPCR. Our findings describe the basic mechanism of FBD disease, right from sensing of phytoplasma infection by host plant triggering molecular signalling leading to mobilization of carbohydrate and protein, phyllody, abnormal pollen development, improved colonization of insect in host plants to spread the disease. Study reveals how phytoplasma hijacks metabolic machinery of soybean manifesting FBD.

CONCLUSIONS

This is the first report of transcriptomic signature of FBD or WBS disease of soybean revealing morphological and metabolic changes which attracts insect for spread of disease. All the genic region putative markers may be used as genomic resource for variety improvement and new agro-chemical development for disease control to enhance soybean productivity.

Characterization and Alternative Splicing Profiles of the Lipoxygenase Gene Family in Tea Plant (Camellia sinensis)

Oxylipins, including jasmonic acid (JA) and volatiles, are important for signaling in plants, and these are formed by the lipoxygenase (LOX) enzyme family. There is a large gap in understanding of the underlying molecular basis of their roles in tea plants. Here, we identified 11 CsLOX genes from the tea plant (Camellia sinensis), and characterized their phylogeny, gene structure and protein features into three subclasses. We then examined their enzymatic activities, LOX expression and alternative splicing of transcripts during development and in response to abiotic or biotic stresses in tea plants. In vitro expressed protein assays showed that the CsLOX2, 3 and 9 enzymatically function to produce 9/13-HPOT, 13-HPOT and 9-HPOT, respectively. CsLOX2 and CsLOX9 green fluorescent protein (GFP) fusion proteins localized to chloroplasts and the cytoplasm, respectively. RNA sequencing, quantitative reverse transcription-PCR and Northern blot analysis suggested that CsLOX5, 6 and 9 were predominantly expressed in seeds, flowers and roots, respectively. CsLOX2, 3, 4, 6 and 7 were up-regulated after attack by the insect Ectropis oblique, while CsLOX1 was induced after infection with the pathogen Glomerella cingulata. CsLOX3, 7 and 10 were up-regulated by JA but not ABA or salicylic acid. Long-term cold stress down-regulated CsLOX expression while a short duration of cold induced the expression of CsLOX1, 6 and 7. Alternatively spliced transcripts of six CsLOX genes were dynamically regulated through time and varied in relative abundances under the investigated stresses; we propose a mechanism of competing or compensating regulation between isoforms. This study improves our understanding of evolution of LOXs and regulation of their diverse functions in plants.

Transcriptome and Expression Profiling Analysis of Recalcitrant Tea (Camellia sinensis L.) Seeds Sensitive to Dehydration

The tea plant (Camellia sinensis (L.) O. Kuntze) is an economically important woody perennial nonalcoholic health beverage crop. Tea seeds are categorized as recalcitrant and are sensitive to dehydration treatment. However, the molecular basis of this phenomenon has not been investigated. Thus, we analyzed the genome-wide expression profiles of three dehydration stages using RNA-Seq and digital gene expression (DGE) technologies. We performed de novo assembly and obtained a total of 91,925 nonredundant unigenes, of which 58,472 were extensively annotated. By a hierarchical clustering of differentially expressed genes (DEGs), we found that 8929 DEGs were downregulated and 5875 DEGs were upregulated during dehydration treatment. A series of genes related to ABA biosynthesis and signal transduction, transcription factor, antioxidant enzyme, LEA protein, and proline metabolism that have been reported to function in dehydration process were found to be downregulated. Additionally, the expression profiles of 12 selected genes related to tea seed dehydration treatment were confirmed by qRT-PCR analysis. To our knowledge, this is the first genome-wide study elucidating the possible molecular mechanisms of sensitivity of recalcitrant tea seeds to dehydration. The results obtained in this study contribute to the preservation of tea seeds as genetic resources and can also be used to explore the mechanism of dehydration sensitivity of other recalcitrant seeds.

Transcriptomic signature of drought response in pearl millet (Pennisetum glaucum (L.) and development of web-genomic resources

Pearl millet, (Pennisetum glaucum L.), an efficient (C4) crop of arid/semi-arid regions is known for hardiness. Crop is valuable for bio-fortification combating malnutrition and diabetes, higher caloric value and wider climatic resilience. Limited studies are done in pot-based experiments for drought response at gene-expression level, but field-based experiment mimicking drought by withdrawal of irrigation is still warranted. We report de novo assembly-based transcriptomic signature of drought response induced by irrigation withdrawal in pearl millet. We found 19983 differentially expressed genes, 7595 transcription factors, gene regulatory network having 45 hub genes controlling drought response. We report 34652 putative markers (4192 simple sequence repeats, 12111 SNPs and 6249 InDels). Study reveals role of purine and tryptophan metabolism in ABA accumulation mediating abiotic response in which MAPK acts as major intracellular signal sensing drought. Results were validated by qPCR of 13 randomly selected genes. We report the first web-based genomic resource ( http://webtom.cabgrid.res.in/pmdtdb/ ) which can be used for candidate genes-based SNP discovery programs and trait-based association studies. Looking at climatic change, nutritional and pharmaceutical importance of this crop, present investigation has immense value in understanding drought response in field condition. This is important in germplasm management and improvement in endeavour of pearl millet productivity.

A Functional Genomic Perspective on Drought Signalling and its Crosstalk with Phytohormone-mediated Signalling Pathways in Plants

INTRODUCTION

Drought stress is one of the most important abiotic stresses that negatively influence crop performance and productivity. Plants acclimatize to drought stress conditions through altered molecular, biochemical and physiological responses. Gene and/or protein expression and regulation are thought to be modulated upon stress perception and signal transduction for providing requisite endurance to plants.Plant growth regulators or phytohormones are important molecules required for various biological processes in plants and are also central to stress signalling pathways. Among various phytohormones, Abscisic Acid (ABA) and Ethylene (ET) are considered to be the most vital growth regulators implicated in drought stress signalling and tolerance. Besides the above two known classical phytohormones, Salicylic Acid (SA) and Jasmonic Acid (JA) have also been found to potentially enhance abiotic stress tolerance particularly that of drought, salinity, and heat stress tolerance in plants. Apart from these several other growth regulators such as Cytokinins (CKs), Auxin (AUX), Gibberellic Acid (GA), Brassinosteroids (BRs) and Strigolactones (SLs) have also been reported to actively participate in abiotic stress responses and tolerance in plants. The abiotic stress signalling in plants regulated by these hormones further depends upon the nature, intensity, and duration of exposure to various environmental stresses. It has been reported that all these phytohormones are also involved in extensive crosstalk and signal transduction among themselves and/or with other factors.

CONCLUSION

This review thus summarizes the molecular mechanism of drought signalling and its crosstalk with various phytohormone signalling pathways implicated in abiotic stress response and tolerance.

Proteomic analysis of Camellia sinensis (L.) reveals a synergistic network in the response to drought stress and recovery

Drought is a crucial limiting factor for tea yield and quality. To systematically characterize the molecular response of tea plants to drought stress and its capacity to recover, we used iTRAQ-based comparative proteomic approach to investigate the effects of drought on protein expression profiles in tea seedlings subjected to different drought treatments. A total of 3274 proteins were identified, of which 2169 and 2300 showed differential expressions during drought and recovery, respectively. Functional annotation showed that multiple biological processes were regulated, suggesting that tea plants probably employed multiple and synergistic resistance mechanisms in dealing with drought stress. Hierarchical clustering showed that chlorophyll a/b-binding proteins were up-regulated in DB and RE, suggesting that tea plants might regulate expression of chlorophyll a/b-binding proteins to maintain the photosystem II function during drought stress. Abundant proteins involved in sulfur-containing metabolite pathways, such as glutathione, taurine, hypotaurine, methionine, and cysteine, changed significantly during drought stress. Among them, TL29 interacted with LHCb6 to connect S-containing metabolites with chlorophyll a/b-binding proteins. This suggests that sulfur-containing compounds play important roles in the response to drought stress in tea plants. In addition, the expression of PAL was up-regulated in DA and down-regulated in DB. Cinnamyl alcohol dehydrogenase, caffeic acid O-methyltransferase, and 4-coumarate-CoA ligase also showed significant changes in expression levels, which regulated the biosynthesis of polyphenols. The results indicate that slight drought stress might promote polyphenol biosynthesis, while serious drought stress leads to inhibition. The expression of lipoxygenase and short-chain dehydrogenase increased during slight drought stress and some volatile metabolite pathways were enriched, indicating that drought stress might affect the tea aroma. The study provides valuable information that will lay the foundation for studies investigating the functions of drought response genes in tea leaves.

Identification of drought-responsive miRNAs and physiological characterization of tea plant (Camellia sinensis L.) under drought stress

BACKGROUND

Drought stress is one of the major natural challenges in the main tea-producing regions of China. The tea plant (Camellia sinensis) is a traditional beverage plant whose growth status directly affects tea quality. Recent studies have revealed that microRNAs (miRNAs) play key functions in plant growth and development. Although some miRNAs have been identified in C. sinensis, little is known about their roles in the drought stress response of tea plants.

RESULTS

Physiological characterization of Camellia sinensis 'Tieguanyin' under drought stress showed that the malondialdehyde concentration and electrical conductivity of leaves of drought-stressed plants increased when the chlorophyll concentration decreased under severe drought stress. We sequenced four small-RNA (sRNA) libraries constructed from leaves of plants subjected to four different treatments, normal water supply (CK); mild drought stress (T1); moderate drought stress (T2) and severe drought stress (T3). A total of 299 known mature miRNA sequences and 46 novel miRNAs were identified. Gene Ontology enrichment analysis revealed that most of the differentially expressed-miRNA target genes were related to regulation of transcription. Kyoto Encyclopedia of Genes and Genomes analysis revealed that the most highly enriched pathways under drought stress were D-alanine metabolism, sulfur metabolism, and mineral absorption pathways. Real-time quantitative PCR (qPCR) was used to validate the expression patterns of 21 miRNAs (2 up-regulated and 19 down-regulated under drought stress). The observed co-regulation of the miR166 family and their targets ATHB-14-like and ATHB-15-like indicate the presence of negative feedback regulation in miRNA pathways.

CONCLUSIONS

Analyses of drought-responsive miRNAs in tea plants showed that most of differentially expressed-miRNA target genes were related to regulation of transcription. The results of study revealed that the expressions of phase-specific miRNAs vary with morphological, physiological, and biochemical changes. These findings will be useful for research on drought resistance and provide insights into the mechanisms of drought adaptation and resistance in C. sinensis.

Transcriptome and metabolite analysis identifies nitrogen utilization genes in tea plant (Camellia sinensis)

Applied nitrogen (N) fertilizer significantly increases the leaf yield. However, most N is not utilized by the plant, negatively impacting the environment. To date, little is known regarding N utilization genes and mechanisms in the leaf production. To understand this, we investigated transcriptomes using RNA-seq and amino acid levels with N treatment in tea (Camellia sinensis), the most popular beverage crop. We identified 196 and 29 common differentially expressed genes in roots and leaves, respectively, in response to ammonium in two tea varieties. Among those genes, AMT, NRT and AQP for N uptake and GOGAT and GS for N assimilation were the key genes, validated by RT-qPCR, which expressed in a network manner with tissue specificity. Importantly, only AQP and three novel DEGs associated with stress, manganese binding, and gibberellin-regulated transcription factor were common in N responses across all tissues and varieties. A hypothesized gene regulatory network for N was proposed. A strong statistical correlation between key genes’ expression and amino acid content was revealed. The key genes and regulatory network improve our understanding of the molecular mechanism of N usage and offer gene targets for plant improvement.

Reliable reference genes for normalization of gene expression data in tea plants (Camellia sinensis) exposed to metal stresses

Tea plants [Camellia sinensis (L.) O. Kuntze] are an important leaf-type crop that are widely used for the production of non-alcoholic beverages in the world. Exposure to excessive amounts of heavy metals adversely affects the quality and yield of tea leaves. To analyze the molecular responses of tea plants to heavy metals, a reliable quantification of gene expression is important and of major importance herein is the normalization of the measured expression levels for the target genes. Ideally, stably expressed reference genes should be evaluated in all experimental systems. In this study, 12 candidate reference genes (i.e., 18S rRNA, Actin, CYP, EF-1α, eIF-4α, GAPDH, MON1, PP2AA3, TBP, TIP41, TUA, and UBC) were cloned from tea plants, and the stability of their expression was examined systematically in 60 samples exposed to diverse heavy metals (i.e., manganese, aluminum, copper, iron, and zinc). Three Excel-based algorithms (geNorm, NormFinder, and BestKeeper) were used to evaluate the expression stability of these genes. PP2AA3 and 18S rRNA were the most stably expressed genes, even though their expression profiles exhibited some variability. Moreover, commonly used reference genes (i.e., GAPDH and TBP) were the least appropriate reference genes for most samples. To further validate the suitability of the analyzed reference genes, the expression level of a phytochelatin synthase gene (i.e., CsPCS1) was determined using the putative reference genes for data normalizations. Our results may be beneficial for future studies involving the quantification of relative gene expression levels in tea plants.

The CsHSP17.2 molecular chaperone is essential for thermotolerance in Camellia sinensis

Small heat shock proteins (sHSPs) play important roles in responses to heat stress. However, the functions of sHSPs in tea plants (Camellia sinensis) remain uncharacterized. A novel sHSP gene, designated CsHSP17.2, was isolated from tea plants. Subcellular localization analyses indicated that the CsHSP17.2 protein was present in the cytosol and the nucleus. CsHSP17.2 expression was significantly up-regulated by heat stress but was unaffected by low temperature. The CsHSP17.2 transcript levels increased following salt and polyethylene glycol 6000 treatments but decreased in the presence of abscisic acid. The molecular chaperone activity of CsHSP17.2 was demonstrated in vitro. Transgenic Escherichia coli and Pichia pastoris expressing CsHSP17.2 exhibited enhanced thermotolerance. The transgenic Arabidopsis thaliana exhibited higher maximum photochemical efficiencies, greater soluble protein proline contents, higher germination rates and higher hypocotyl elongation length than the wild-type controls. The expression levels of several HS-responsive genes increased in transgenic A. thaliana plants. Additionally, the CsHSP17.2 promoter is highly responsive to high-temperature stress in A. thaliana. Our results suggest that CsHSP17.2 may act as a molecular chaperone to mediate heat tolerance by maintaining maximum photochemical efficiency and protein synthesis, enhancing the scavenging of reactive oxygen species and inducing the expression of HS-responsive genes.

Global Transcriptional Analysis Reveals the Complex Relationship between Tea Quality, Leaf Senescence and the Responses to Cold-Drought Combined Stress in Camellia sinensis

In field conditions, especially in arid and semi-arid areas, tea plants are often simultaneously exposed to various abiotic stresses such as cold and drought, which have profound effects on leaf senescence process and tea quality. However, most studies of gene expression in stress responses focus on a single inciting agent, and the confounding effect of multiple stresses on crop quality and leaf senescence remain unearthed. Here, global transcriptome profiles of tea leaves under separately cold and drought stress were compared with their combination using RNA-Seq technology. This revealed that tea plants shared a large overlap in unigenes displayed "similar" (26%) expression pattern and avoid antagonistic responses (lowest level of "prioritized" mode: 0%) to exhibit very congruent responses to co-occurring cold and drought stress; 31.5% differential expressed genes and 38% of the transcriptome changes in response to combined stresses were unpredictable from cold or drought single-case studies. We also identified 319 candidate genes for enhancing plant resistance to combined stress. We then investigated the combined effect of cold and drought on tea quality and leaf senescence. Our results showed that drought-induced leaf senescence were severely delayed by (i) modulation of a number of senescence-associated genes and cold responsive genes, (ii) enhancement of antioxidant capacity, (iii) attenuation of lipid degradation, (iv) maintenance of cell wall and photosynthetic system, (v) alteration of senescence-induced sugar effect/sensitivity, as well as (vi) regulation of secondary metabolism pathways that significantly influence the quality of tea during combined stress. Therefore, care should be taken when utilizing a set of stresses to try and maximize leaf longevity and tea quality.

Transcriptomic Changes of Drought-Tolerant and Sensitive Banana Cultivars Exposed to Drought Stress

In banana, drought responsive gene expression profiles of drought-tolerant and sensitive genotypes remain largely unexplored. In this research, the transcriptome of drought-tolerant banana cultivar (Saba, ABB genome) and sensitive cultivar (Grand Naine, AAA genome) was monitored using mRNA-Seq under control and drought stress condition. A total of 162.36 million reads from tolerant and 126.58 million reads from sensitive libraries were produced and mapped onto the Musa acuminata genome sequence and assembled into 23,096 and 23,079 unigenes. Differential gene expression between two conditions (control and drought) showed that at least 2268 and 2963 statistically significant, functionally known, non-redundant differentially expressed genes (DEGs) from tolerant and sensitive libraries. Drought has up-regulated 991 and 1378 DEGs and down-regulated 1104 and 1585 DEGs respectively in tolerant and sensitive libraries. Among DEGs, 15.9% are coding for transcription factors (TFs) comprising 46 families and 9.5% of DEGs are constituted by protein kinases from 82 families. Most enriched DEGs are mainly involved in protein modifications, lipid metabolism, alkaloid biosynthesis, carbohydrate degradation, glycan metabolism, and biosynthesis of amino acid, cofactor, nucleotide-sugar, hormone, terpenoids and other secondary metabolites. Several, specific genotype-dependent gene expression pattern was observed for drought stress in both cultivars. A subset of 9 DEGs was confirmed using quantitative reverse transcription-PCR. These results will provide necessary information for developing drought-resilient banana plants.