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.

Tea [Camellia sinensis (L) O. Kuntze, Theaceae] is one of the most popular non-alcoholic beverages worldwide. Cold stress is one of the most severe abiotic stresses that limit tea plants’ growth, survival and geographical distribution. However, the genetic regulatory network and signaling pathways involved in cold stress responses in tea plants remain unearthed. Using RNA-Seq, DGE and sRNA-Seq technologies, we performed an integrative analysis of miRNA and mRNA expression profiling and their regulatory network of tea plants under chilling (4℃) and freezing (-5℃) stress. Differentially expressed (DE) miRNA and mRNA profiles were obtained based on fold change analysis, miRNAs and target mRNAs were found to show both coherent and incoherent relationships in the regulatory network. Furthermore, we compared several key pathways (e.g., ‘Photosynthesis’), GO terms (e.g., ‘response to karrikin’) and transcriptional factors (TFs, e.g., DREB1b/CBF1) which were identified as involved in the early chilling and/or freezing response of tea plants. Intriguingly, we found that karrikins, a new group of plant growth regulators, and β-primeverosidase (BPR), a key enzyme functionally relevant with the formation of tea aroma might play an important role in both early chilling and freezing response of tea plants. Quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) analysis further confirmed the results from RNA-Seq and sRNA-Seq analysis. This is the first study to simultaneously profile the expression patterns of both miRNAs and mRNAs on a genome-wide scale to elucidate the molecular mechanisms of early responses of tea plants to cold stress. In addition to gaining a deeper insight into the cold resistant characteristics of tea plants, we provide a good case study to analyse mRNA/miRNA expression and profiling of non-model plant species using next-generation sequencing technology.

The effects of blue (BL) and green light (GL) treatment during the dark period were examined in Camellia sinensis as a first step to understanding the spectral effects of artificial BL and GL on plant secondary metabolism and light signaling interactions. BL could induce the expression of CRY2/3, SPAs, HY5, and R2R3-MYBs to promote the accumulation of anthocyanins and catechins in tea plants. GL, on the other hand, could stimulate the accumulation of several functional substances (e.g., procyanidin B2/B3 and l-ascorbate) and temper these BL responses via down-regulation of CRY2/3 and PHOT2. Furthermore, the molecular events that triggered by BL and GL signals were partly overlapped with abiotic/biotic stress responses. We indicate the possibility of a targeted use of BL and GL to regulate the amount of functional metabolites to enhance tea quality and taste, and to potentially trigger defense mechanisms of tea plants.

Tea is one of the most popular nonalcoholic beverages due to its characteristic secondary metabolites with numerous health benefits. Although two draft genomes of tea plant (Camellia sinensis) have been published recently, the lack of chromosome-scale assembly hampers the understanding of the fundamental genomic architecture of tea plant and potential improvement. Here, we performed a genome-wide chromosome conformation capture technique (Hi-C) to obtain a chromosome-scale assembly based on the draft genome of C. sinensis var. sinensis and successfully ordered 2984.7 Mb (94.7%) scaffolds into 15 chromosomes. The scaffold N50 of the improved genome was 218.1 Mb,~157-fold higher than that of the draft genome. Collinearity comparison of genome sequences and two genetic maps validated the high contiguity and accuracy of the chromosome-scale assembly. We clarified that only one Camellia recent tetraploidization event (CRT, 58.9-61.7 million years ago (Mya)) occurred after the core-eudicot common hexaploidization event (146.6-152.7 Mya). Meanwhile, 9243 genes (28.6%) occurred in tandem duplication, and most of these expanded after the CRT event. These gene duplicates increased functionally divergent genes that play important roles in tea-specific biosynthesis or stress response. Sixty-four catechin-and caffeine-related quantitative trait loci (QTLs) were anchored to chromosome assembly. Of these, two catechin-related QTL hotspots were derived from the CRT event, which illustrated that polyploidy has played a dramatic role in the diversification of tea germplasms. The availability of a chromosome-scale genome of tea plant holds great promise for the understanding of genome evolution and the discovery of novel genes contributing to agronomically beneficial traits in future breeding programs.

Highlights d Chromatin priming of immune genes in OLG in homeostasis and disease d BACH1, STAT1, and Polycomb involved in IFN-g-mediated immune gene regulation in OPCs d MS susceptibility SNPs overlap with open chromatin regions in OLG d IFN-g leads to altered chromatin and gene expression at SNP loci in mouse OPCs

No abstract

Tea plant (Camellia sinensis (L) O. Kuntze) respond to herbivore attack through large changes in defense related metabolism and gene expression. Ectropis oblique (Prout) is one of the most devastating insects that feed on tea leaves and tender buds, which can cause severe production loss and deteriorate the quality of tea. To elucidate the biochemicals and molecular mechanism of defense against tea geometrid (TG), transcriptome and metabolome of TG interaction with susceptible (SG) and resistance (RG) tea genotypes were analyzed by using UPLC-Q-TOF-MS, GC-MS, and RNA-seq technologies. This revealed that jasmonic acid was highly induced in RG, following a plethora of secondary metabolites involved in defense against TG could be induced by jasmonic acid signaling pathway. However, the constitutively present of salicylic acid in SG might be a suppressor of jasmonate signaling and thus misdirect tea plants against TG. Furthermore, flavonoids and terpenoids biosynthesis pathways were highly activated in RG to constitute the chemical barrier on TG feeding behavior. In contrast, fructose and theanine, which can act as feeding stimulants were observed to highly accumulate in SG. Being present in the major hub, 39 transcription factors or protein kinases among putative candidates were identified as master regulators from protein-protein interaction network analysis. Together, the current study provides a comprehensive gene expression and metabolite profiles, which can shed new insights into the molecular mechanism of tea defense against TG. The candidate genes and specific metabolites identified in the present study can serve as a valuable resource for unraveling the possible defense mechanism of plants against various biotic stresses.

Following the recent completion of the draft genome sequence of the tea plant, high-throughput decoding of gene function, especially for those involved in complex secondary metabolic pathways, has become a major challenge. Here, we profiled the metabolome and transcriptome of 11 tea cultivars, and then illustrated a weighted gene coexpression network analysis (WGCNA)-based system biological strategy to interpret metabolomic flux, predict gene functions, and mine key regulators involved in the flavonoid biosynthesis pathway. We constructed a multilayered regulatory network, which integrated the gene coexpression relationship with the microRNA target and promoter cis-regulatory element information. This allowed us to reveal new uncharacterized TFs (e.g., MADSs, WRKYs, and SBPs) and microRNAs (including 17 conserved and 15 novel microRNAs) that are potentially implicated in different steps of the catechin biosynthesis. Furthermore, we applied metabolicsignature-based association method to capture additional key regulators involved in catechin pathway. This provides important clues for the functional characterization of five SCPL1A acyltransferase family members, which might be implicated in the production balance of anthocyanins, galloylated catechins, and proanthocyanins. Application of an "omics"-based system biology strategy should facilitate germplasm utilization and provide valuable resources for tea quality improvement.