Transcriptome-wide identification of Camellia sinensis WRKY transcription factors in response to temperature stress

Comparative transcriptomic and metabolomic analyses provide insights into the responses to high temperature stress in Alfalfa (Medicago sativa L.)

High temperature stress is one of the most severe forms of abiotic stress in alfalfa. With the intensification of climate change, the frequency of high temperature stress will further increase in the future, which will bring challenges to the growth and development of alfalfa. Therefore, untargeted metabolomic and RNA-Seq profiling were implemented to unravel the possible alteration in alfalfa seedlings subjected to different temperature stress (25 ℃, 30 ℃, 35 ℃, 40 ℃) in this study. Results revealed that High temperature stress significantly altered some pivotal transcripts and metabolites. The number of differentially expressed genes (DEGs) markedly up and down-regulated was 1876 and 1524 in T30_vs_CK, 2, 815 and 2667 in T35_vs_CK, and 2115 and 2, 226 in T40_vs_CK, respectively. The number for significantly up-regulated and down-regulated differential metabolites was 173 and 73 in T30_vs_CK, 188 and 57 in T35_vs_CK, and 220 and 66 in T40_vs_CK, respectively. It is worth noting that metabolomics and transcriptomics co-analysis characterized enriched in plant hormone signal transduction (ko04705), glyoxylate and dicarboxylate metabolism (ko00630), from which some differentially expressed genes and differential metabolites participated. In particular, the content of hormone changed significantly under T40 stress, suggesting that maintaining normal hormone synthesis and metabolism may be an important way to improve the HTS tolerance of alfalfa. The qRT-PCR further showed that the expression pattern was similar to the expression abundance in the transcriptome. This study provides a practical and in-depth perspective from transcriptomics and metabolomics in investigating the effects conferred by temperature on plant growth and development, which provided the theoretical basis for breeding heat-resistant alfalfa.

Genome-Wide Identification and Analysis of MYB Transcription Factors in Pyropia yezoensis

MYB transcription factors are one of the largest transcription factor families in plants, and they regulate numerous biological processes. Red algae are an important taxonomic group and have important roles in economics and research. However, no comprehensive analysis of the MYB gene family in any red algae, including Pyropia yezoensis, has been conducted. To identify the MYB gene members of Py. yezoensis, and to investigate their family structural features and expression profile characteristics, a study was conducted. In this study, 3 R2R3-MYBs and 13 MYB-related members were identified in Py. yezoensis. Phylogenetic analysis indicated that most red algae MYB genes could be clustered with green plants or Glaucophyta MYB genes, inferring their ancient origins. Synteny analysis indicated that 13 and 5 PyMYB genes were orthologous to Pyropia haitanensis and Porphyra umbilicalis, respectively. Most Bangiaceae MYB genes contain several Gly-rich motifs, which may be the result of an adaptation to carbon limitations and maintenance of important regulatory functions. An expression profile analysis showed that PyMYB genes exhibited diverse expression profiles. However, the expression patterns of different members appeared to be diverse, and PyMYB5 was upregulated in response to dehydration, low temperature, and Pythium porphyrae infection. This is the first comprehensive study of the MYB gene family in Py. Yezoensis and it provides vital insights into the functional divergence of MYB genes.

Plant salinity stress, sensing, and its mitigation through WRKY

Salinity or salt stress has deleterious effects on plant growth and development. It imposes osmotic, ionic, and secondary stresses, including oxidative stress on the plants and is responsible for the reduction of overall crop productivity and therefore challenges global food security. Plants respond to salinity, by triggering homoeostatic mechanisms that counter salt-triggered disturbances in the physiology and biochemistry of plants. This involves the activation of many signaling components such as SOS pathway, ABA pathway, and ROS and osmotic stress signaling. These biochemical responses are accompanied by transcriptional modulation of stress-responsive genes, which is mostly mediated by salt-induced transcription factor (TF) activity. Among the TFs, the multifaceted significance of WRKY proteins has been realized in many diverse avenues of plants' life including regulation of plant stress response. Therefore, in this review, we aimed to highlight the significance of salinity in a global perspective, the mechanism of salt sensing in plants, and the contribution of WRKYs in the modulation of plants' response to salinity stress. This review will be a substantial tool to investigate this problem in different perspectives, targeting WRKY and offering directions to better manage salinity stress in the field to ensure food security.

Genome-Wide Identification and Analysis of the WRKY Gene Family in Asparagus officinalis

In recent years, the related research of the WRKY gene family has been gradually promoted, which is mainly reflected in the aspects of environmental stress and hormone response. However, to make the study of the WRKY gene family more complete, we also need to focus on the whole-genome analysis and identification of the family. In previous studies, the whole WRKY gene family of Arabidopsis, legumes and other plants has been thoroughly studied. However, since the publication of Asparagus officinalis genome-wide data, there has never been an analysis of the whole WRKY gene family. To understand more broadly the function of the WRKY gene family, the whole genome and salt stress transcriptome data of asparagus were used for comprehensive analysis in this study, including WRKY gene family identification, phylogenetic tree construction, analysis of conserved mods and gene domains, extraction of cis-acting elements, intron/exon analysis, species collinearity analysis, and WRKY expression analysis under salt stress. The results showed that a total of 70 genes were selected and randomly distributed on 10 chromosomes and one undefined chromosome. According to the functional classification of Arabidopsis thaliana, the WRKY family of asparagus was divided into 11 subgroups (C1-C9, U1, U2). It is worth considering that the distribution rules of gene-conserved motifs, gene domains and introns/exons in the same subfamily are similar, which suggests that genes in the same subfamily may regulate similar physiological processes. In this study, 11 cis-acting elements of WRKY family were selected, among which auxin, gibberellin, abscisic acid, salicylic acid and other hormone-regulated induction elements were involved. In addition, environmental stress (such as drought stress and low-temperature response) also accounted for a large proportion. Interestingly, we analyzed a total of two tandem duplicate genes and 13 segmental duplication genes, suggesting that this is related to the amplification of the WRKY gene family. Transcriptome data analysis showed that WRKY family genes could regulate plant growth and development by up-regulating and down-regulating gene expression under salt stress. Volcanic maps showed that 3 and 15 AoWRKY genes were significantly up-regulated or down-regulated in NI&NI+S and AMF&AMF+S, respectively. These results provide a new way to analyze the evolution and function of the WRKY gene family, and can provide a reference for the production and research of asparagus.

Multi-algorithm cooperation research of WRKY genes under nitrogen stress in Panax notoginseng

WRKY transcription factors play an important role in the immune system and the innate defense response of plants. WRKY transcription factors have great feedback on nitrogen stress. In this study, bioinformatics was used to detect the WRKYs of Panax notoginseng (PnWRKYs). The response of PnWRKYs under nitrogen stress was also well studied. PnWRKYs were distributed on 11 chromosomes. According to PnWRKY and Arabidopsis thaliana WRKY (AtWRKY) domains, these PnWRKY proteins were divided into three groups by phylogenetic analysis. MEME analysis showed that almost every member contained motif 1 and motif 2. PlantCARE online predicted the cis-acting elements of the promoter. PnWRKY gene family members obtained 22 pairs of repeat fragments by collinearity analysis. The expression levels of PnWRKYs in different parts (roots, flowers, and leafs) were analyzed by the gene expression pattern. They reflected tissue-specific expressions. The qRT-PCR experiments were used to detect 74 PnWRKYs under nitrogen stress. The results showed that the expression levels of 8 PnWRKYs were significantly induced. The PnWRKY gene family may be involved in biotic/abiotic stresses and hormone induction. This study will not only lay the foundation to explore the functions of PnWRKYs but also provide candidate genes for the future improvement of P. notoginseng.

Exogenous methyl jasmonate and cytokinin antagonistically regulate lignin biosynthesis by mediating CsHCT expression in Camellia sinensis

Tea plant, an important beverage crop, is cultivated worldwide. Lignification can improve the hardness of tea plant, which is of great significance for tea quality. Jasmonates (JAs) and cytokinin are plant hormones that control processes of plant development and secondary metabolite accumulation. Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase (HCT) is primarily involved in lignin biosynthesis. The effects of exogenous application of JAs and cytokinin on lignin biosynthesis and related HCT gene expression profiles in tea plants are still unclear. In order to investigate the effects of exogenous JAs and cytokinin on lignin accumulation, anatomical structures, and CsHCT gene profiles in tea plants, we treated tea plants with methyl jasmonate (MeJA) and cytokinin (6-BA). MeJA and 6-BA treatments triggered the lignification at 6 and 12 d in tea leaves. The combined treatment resulted in an increase in lignin content at 6 d, which was 1.32 times of that at 0 d for 'Mengshan 9.' The CsHCTs in clade 2 (CsHCT5, CsHCT6, CsHCT7, and CsHCT8) were mainly expressed in leaves. We found that exogenous MeJA and cytokinin might be able to antagonistically regulate tea plant lignin accumulation through the mediation of CsHCT expression. This study revealed that HCTs play potential important roles involved in lignin biosynthesis of tea plant development and hormonal stimuli.

Progress in the understanding of WRKY transcription factors in woody plants

The WRKY transcription factor (TF) family, named for its iconic WRKY domain, is among the largest and most functionally diverse TF families in higher plants. WRKY TFs typically interact with the W-box of the target gene promoter to activate or inhibit the expression of downstream genes; these TFs are involved in the regulation of various physiological responses. Analyses of WRKY TFs in numerous woody plant species have revealed that WRKY family members are broadly involved in plant growth and development, as well as responses to biotic and abiotic stresses. Here, we review the origin, distribution, structure, and classification of WRKY TFs, along with their mechanisms of action, the regulatory networks in which they are involved, and their biological functions in woody plants. We consider methods currently used to investigate WRKY TFs in woody plants, discuss outstanding problems, and propose several new research directions. Our objective is to understand the current progress in this field and provide new perspectives to accelerate the pace of research that enable greater exploration of the biological functions of WRKY TFs.

Genome-wide analysis of WRKY transcription factor genes in Toona sinensis: An insight into evolutionary characteristics and terpene synthesis

WRKY transcription factors (TFs), one of the largest TF families, serve critical roles in the regulation of secondary metabolite production. However, little is known about the expression pattern of WRKY genes during the germination and maturation processes of Toona sinensis buds. In the present study, the new assembly of the T. sinensis genome was used for the identification of 78 TsWRKY genes, including gene structures, phylogenetic features, chromosomal locations, conserved protein domains, cis-regulatory elements, synteny, and expression profiles. Gene duplication analysis revealed that gene tandem and segmental duplication events drove the expansion of the TsWRKYs family, with the latter playing a key role in the creation of new TsWRKY genes. The synteny and evolutionary constraint analyses of the WRKY proteins among T. sinensis and several distinct species provided more detailed evidence of gene evolution for TsWRKYs. Besides, the expression patterns and co-expression network analysis show TsWRKYs may multi-genes co-participate in regulating terpenoid biosynthesis. The findings revealed that TsWRKYs potentially play a regulatory role in secondary metabolite synthesis, forming the basis for further functional characterization of WRKY genes with the intention of improving T. sinensis.

Transcriptome Profiling of Stem-Differentiating Xylem in Response to Abiotic Stresses Based on Hybrid Sequencing in Cunninghamia lanceolata

Cunninghamia lanceolata (C. lanceolata) belongs to Gymnospermae, which are fast-growing and have desirable wood properties. However, C. lanceolata's stress resistance is little understood. To unravel the physiological and molecular regulation mechanisms under environmental stresses in the typical gymnosperm species of C. lanceolata, three-year-old plants were exposed to simulated drought stress (polyethylene glycol 8000), salicylic acid, and cold treatment at 4 °C for 8 h, 32 h, and 56 h, respectively. Regarding the physiological traits, we observed a decreased protein content and increased peroxidase upon salicylic acid and polyethylene glycol treatment. Superoxide dismutase activity either decreased or increased at first and then returned to normal under the stresses. Regarding the molecular regulation, we used both nanopore direct RNA sequencing and short-read sequencing to reveal a total of 5646 differentially expressed genes in response to different stresses, of which most had functions in lignin catabolism, pectin catabolism, and xylan metabolism, indicating that the development of stem-differentiating xylem was affected upon stress treatment. Finally, we identified a total of 51 AP2/ERF, 29 NAC, and 37 WRKY transcript factors in C. lanceolata. The expression of most of the NAC TFs increased under cold stress, and the expression of most of the WRKY TFs increased under cold and SA stress. These results revealed the transcriptomics responses in C. lanceolata to short-term stresses under this study's experimental conditions and provide preliminary clues about stem-differentiating xylem changes associated with different stresses.

Characterization of the WRKY gene family in Akebia trifoliata and their response to Colletotrichum acutatum

BACKGROUND

Akebia trifoliata, belonging to the Lardizabalaceae family, is a well-known Chinese traditional medicinal plant, susceptible to many diseases, such as anthracnose and powdery mildew. WRKY is one of the largest plant-specific transcription factor families and plays important roles in plant growth, development and stress response, especially in disease resistance. However, little was known about the numbers, characters, evolutionary relationship and expression of WRKY genes in A. trifoliata in response to plant disease due to lacking of A. trifoliata genome.

RESULTS

A total of 42 putative AktWRKY genes were identified based on the full-length transcriptome-sequencing data of A. trifoliata. Then 42 AktWRKY genes were divided into three major groups (Group I-III) based on the WRKY domains. Motif analysis showed members within same group shared a similar motif composition, implying a functional conservation. Tissue-specific expression analysis showed that AktWRKY genes could be detected in all tissues, while few AktWRKY genes were tissue specific. We further evaluated the expression of AktWRKY genes in three varieties in response to Colletotrichum acutatum by qRT-PCR. The expression patterns of AktWRKY genes were similar between C01 and susceptible variety I02, but distinctly different in resistant variety H05. In addition, it showed that more than 64 percentages of AktWRKY genes were differentially expressed during fungal infection in I02 and H05. Furthermore, Gene ontology (GO) analysis showed that AktWRKY genes were categorized into 26 functional groups under cellular components, molecular functions and biological processes, and a predicted protein interaction network was also constructed.

CONCLUSIONS

Results of bioinformation analysis and expression patterns implied that AktWRKYs might play multiple function in response to biotic stresses. Our study could facilitate to further investigate the function and regulatory mechanism of the WRKY in A. trifoliata during pathogen response.

Unfolding molecular switches in plant heat stress resistance: A comprehensive review

Plant heat stress response is a multi-factorial trait that is precisely regulated by the complex web of transcription factors from various families that modulate heat stress responsive gene expression. Global warming due to climate change affects plant growth and development throughout its life cycle. Adds to this, the frequent occurrence of heat waves is drastically reducing the global crop yield. Molecular plant scientists can help crop breeders by providing genetic markers associated with stress resistance. Plant heat stress response (HSR), however, is a multi-factorial trait and using a single stress resistance trait might not be ideal to develop thermotolerant crops. Transcription factors participate in regulation of plant biological processes and environmental stress responses. Recent studies have revealed that plant HSR is precisely regulated by the complex web of transcription factors from various families. These transcription factors enhance plant heat stress tolerance by regulating the expression level of several stress-responsive genes independently or in cross talk with different other transcription factors. This review explores how signaling pathways triggered by heat stress are regulated by multiple transcription factor families. To our knowledge, we for the first time analyze the role of major transcription factor families in plant HSR along with their regulatory mechanisms. In the end, we will also discuss the potential of emerging technologies to improve thermotolerance in plants.

Identification and Expression Analysis of WRKY Gene Family in Response to Abiotic Stress in Dendrobium catenatum

Dendrobium catenatum has become a rare and endangered medicinal plant due to habitat loss in China. As one of the most important and largest transcription factors, WRKY plays a critical role in response to abiotic stresses in plants. However, little is known regarding the functions of the WRKY family in D. catenatum. In this study, a total of 62 WRKY genes were identified from the D. catenatum genome. Phylogenetic analysis revealed that DcWRKY proteins could be divided into three groups, a division supported by the conserved motif compositions and intron/exon structures. DcWRKY gene expression and specific responses under drought, heat, cold and salt stresses were analyzed through RNA-seq data and RT-qPCR assay. The results showed that these genes had tissue-specificity and displayed different expression patterns in response to abiotic stresses. The expression levels of DcWRKY22, DcWRKY36 and DcWRKY45 were up-regulated by drought stress. Meanwhile, DcWRKY22 was highly induced by heat in roots, and DcWRKY45 was significantly induced by cold stress in leaves. Furthermore, DcWRKY27 in roots and DcWRKY58 in leaves were extremely induced under salt treatment. Finally, we found that all the five genes may function in ABA- and SA-dependent manners. This study identified candidate WRKY genes with possible roles in abiotic stress and these findings not only contribute to our understanding of WRKY family genes, but also provide valuable information for stress resistance development in D. catenatum.

Genome-wide identification and characterization of functionally relevant microsatellite markers from transcription factor genes of Tea (Camellia sinensis (L.) O. Kuntze)

Tea, being one of the most popular beverages requires large set of molecular markers for genetic improvement of quality, yield and stress tolerance. Identification of functionally relevant microsatellite or simple sequence repeat (SSR) marker resources from regulatory “Transcription factor (TF) genes” can be potential targets to expedite molecular breeding efforts. In current study, 2776 transcripts encoding TFs harbouring 3687 SSR loci yielding 1843 flanking markers were identified from traits specific transcriptome resource of 20 popular tea cultivars. Of these, 689 functionally relevant SSR markers were successfully validated and assigned to 15 chromosomes (Chr) of CSS genome. Interestingly, 589 polymorphic markers including 403 core-set of TF-SSR markers amplified 2864 alleles in key TF families (bHLH, WRKY, MYB-related, C2H2, ERF, C3H, NAC, FAR1, MYB and G2-like). Their significant network interactions with key genes corresponding to aroma, quality and stress tolerance suggests their potential implications in traits dissection. Furthermore, single amino acid repeat reiteration in CDS revealed presence of favoured and hydrophobic amino acids. Successful deployment of markers for genetic diversity characterization of 135 popular tea cultivars and segregation in bi-parental population suggests their wider utility in high-throughput genotyping studies in tea.

Genome-Wide Identification and Analysis of the WRKY Gene Family and Cold Stress Response in Acer truncatum

WRKY transcription factors constitute one of the largest gene families in plants and are involved in many biological processes, including growth and development, physiological metabolism, and the stress response. In earlier studies, the WRKY gene family of proteins has been extensively studied and analyzed in many plant species. However, information on WRKY transcription factors in Acer truncatum has not been reported. In this study, we conducted genome-wide identification and analysis of the WRKY gene family in A. truncatum, 54 WRKY genes were unevenly located on all 13 chromosomes of A. truncatum, the highest number was found in chromosomes 5. Phylogenetic relationships, gene structure, and conserved motif identification were constructed, and the results affirmed 54 AtruWRKY genes were divided into nine subgroup groups. Tissue species analysis of AtruWRKY genes revealed which were differently exhibited upregulation in flower, leaf, root, seed and stem, and the upregulation number were 23, 14, 34, 18, and 8, respectively. In addition, the WRKY genes expression in leaf under cold stress showed that more genes were significantly expressed under 0, 6 and 12 h cold stress. The results of this study provide a new insight the regulatory function of WRKY genes under abiotic and biotic stresses.

WRKY Transcription Factor Response to High-Temperature Stress

Plant growth and development are closely related to the environment, and high-temperature stress is an important environmental factor that affects these processes. WRKY transcription factors (TFs) play important roles in plant responses to high-temperature stress. WRKY TFs can bind to the W-box cis-acting elements of target gene promoters, thereby regulating the expression of multiple types of target genes and participating in multiple signaling pathways in plants. A number of studies have shown the important biological functions and working mechanisms of WRKY TFs in plant responses to high temperature. However, there are few reviews that summarize the research progress on this topic. To fully understand the role of WRKY TFs in the response to high temperature, this paper reviews the structure and regulatory mechanism of WRKY TFs, as well as the related signaling pathways that regulate plant growth under high-temperature stress, which have been described in recent years, and this paper provides references for the further exploration of the molecular mechanisms underlying plant tolerance to high temperature.

WRKY transcription factors and plant defense responses: latest discoveries and future prospects

WRKY transcription factors are among the largest families of transcriptional regulators. In this review, their pivotal role in modulating various signal transduction pathways during biotic and abiotic stresses is discussed. Transcription factors (TFs) are important constituents of plant signaling pathways that define plant responses against biotic and abiotic stimuli besides playing a role in response to internal signals which coordinate different interacting partners during developmental processes. WRKY TFs, deriving their nomenclature from their signature DNA-binding sequence, represent one of the largest families of transcriptional regulators found exclusively in plants. By modulating different signal transduction pathways, these TFs contribute to various plant processes including nutrient deprivation, embryogenesis, seed and trichome development, senescence as well as other developmental and hormone-regulated processes. A growing body of research suggests transcriptional regulation of WRKY TFs in adapting plant to a variety of stressed environments. WRKY TFs can regulate diverse biological functions from receptors for pathogen triggered immunity, modulator of chromatin for specific interaction and signal transfer through a complicated network of genes. Latest discoveries illustrate the interaction of WRKY proteins with other TFs to form an integral part of signaling webs that regulate several seemingly disparate processes and defense-related genes, thus establishing their significant contributions to plant immune response. The present review starts with a brief description on the structural characteristics of WRKY TFs followed by the sections that present recent evidence on their roles in diverse biological processes in plants. We provide a comprehensive overview on regulatory crosstalks involving WRKY TFs during multiple stress responses in plants and future prospects of WRKY TFs as promising molecular diagnostics for enhancing crop improvement.

Underpinning the molecular programming attributing heat stress associated thermotolerance in tea (Camellia sinensis (L.) O. Kuntze)

The most daunting issue of global climate change is the deleterious impact of extreme temperatures on tea productivity and quality, which has resulted in a quest among researchers and growers. The current study aims to unravel molecular programming underpinning thermotolerance by characterizing heat tolerance and sensitivity response in 20 tea cultivars. The significantly higher negative influence of heat stress was recorded in a sensitive cultivar with reduced water retention (47%), chlorophyll content (33.79%), oxidation potential (32.48%), and increase in membrane damage (76.4%). Transcriptional profiling of most tolerant and sensitive cultivars identified 78 differentially expressed unigenes with chaperon domains, including low and high molecular weight heat shock protein (HSP) and heat shock transcription factors (HSFs) involved in heat shock response (HSR). Further, predicted transcriptional interactome network revealed their key role in thermotolerance via well-co-ordinated transcriptional regulation of aquaporins, starch metabolism, chlorophyll biosynthesis, calcium, and ethylene mediated plant signaling system. The study identified the key role of HSPs (CsHSP90) in regulating HSR in tea, wherein, structure-based molecular docking revealed the inhibitory role of geldanamycin (GDA) on CsHSP90 by blocking ATP binding site at N-terminal domain of predicted structure. Subsequently, GDA mediated leaf disc inhibitor assay further affirmed enhanced HSR with higher expression of CsHSP17.6, CsHSP70, HSP101, and CsHSFA2 genes in tea. Through the current study, efforts were made to extrapolate a deeper understanding of chaperons mediated regulation of HSR attributing thermotolerance in tea.

Genome-Wide Transcriptomic Identification and Functional Insight of Lily WRKY Genes Responding to Botrytis Fungal Disease

Genome-wide transcriptome analysis using RNA-Seq of Lilium longiflorum revealed valuable genes responding to biotic stresses. WRKY transcription factors are regulatory proteins playing essential roles in defense processes under environmental stresses, causing considerable losses in flower quality and production. Thirty-eight WRKY genes were identified from the transcriptomic profile from lily genotypes, exhibiting leaf blight caused by Botrytis elliptica. Lily WRKYs have a highly conserved motif, WRKYGQK, with a common variant, WRKYGKK. Phylogeny of LlWRKYs with homologous genes from other representative plant species classified them into three groups- I, II, and III consisting of seven, 22, and nine genes, respectively. Base on functional annotation, 22 LlWRKY genes were associated with biotic stress, nine with abiotic stress, and seven with others. Sixteen unique LlWRKY were studied to investigate responses to stress conditions using gene expression under biotic and abiotic stress treatments. Five genes-LlWRKY3, LlWRKY4, LlWRKY5, LlWRKY10, and LlWRKY12-were substantially upregulated, proving to be biotic stress-responsive genes in vivo and in vitro conditions. Moreover, the expression patterns of LlWRKY genes varied in response to drought, heat, cold, and different developmental stages or tissues. Overall, our study provides structural and molecular insights into LlWRKY genes for use in the genetic engineering in Lilium against Botrytis disease.

Transcriptome-wide identification of WRKY family genes and their expression profiling toward salicylic acid in Camellia japonica

The ornamental plant Camellia japonica is widely distributed worldwide and is susceptible to various environmental stresses. The WRKY transcription factor (TF) is an important node of plant tolerance. However, WRKY TFs from C. japonica have not been reported yet. In this study, 48 CjWRKYs, namely, CjWRKY1 to CjWRKY48, were identified. Protein structure analysis revealed that CjWRKY proteins contain a highly conserved motif (WRKYGQK) and two variant motifs (WRKYGKK and WRKYGRK). Phylogenetic analysis indicated that the 48 CjWRKYs can be divided into three groups, which are further classified into six subgroups, namely, I-C, II-a, II-b, II-c, II-e, and III, which contain 10, 6, 8, 13, 7, and 4 members, respectively. The expression patterns of 15 CjWRKYs under salicylic acid (SA) treatment were investigated by real-time quantitative PCR (qRT-PCR). Results showed that the 15 CjWRKYs could be induced by SA treatment. This study is the first to screen CjWRKYs and identify the expression profile of CjWRKYs under SA treatment and provides a theoretical basis for analyzing the function of CjWRKY genes to SA stress tolerance in C. japonica.

Transcriptome-Wide Identification of WRKY Transcription Factors and Their Expression Profiles under Different Types of Biological and Abiotic Stress in Pinus massoniana Lamb

Pinus massoniana Lamb, an economically important conifer tree, is widely distributed in China. WRKY transcription factors (TFs) play important roles in plant growth and development, biological and abiotic stress. Nevertheless, there is little information about the WRKY genes in P. massoniana. By searching for conserved WRKY motifs in transcriptomic RNA sequencing data for P. massoniana, 31 sequences were identified as WRKY TFs. Then, phylogenetic and conserved motif analyses of the WRKY family in P. massoniana, Pinus taeda and Arabidopsis thaliana were used to classify WRKY genes. The expression patterns of six PmWRKY genes from different groups were determined using real-time quantitative PCR for 2-year-old P. massoniana seedings grown in their natural environment and challenged by phytohormones (salicylic acid, methyl jasmonate, or ethephon), abiotic stress (H₂O₂) and mechanical damage stress. As a result, the 31 PmWRKY genes identified were divided into three major groups and several subgroups based on structural and phylogenetic features. PmWRKY genes are regulated in response to abiotic stress and phytohormone treatment and may participate in signaling to improve plant stress resistance. Some PmWRKY genes behaved as predicted based on their homology with A. thaliana WRKY genes, but others showed divergent behavior. This systematic analysis lays the foundation for further identification of WRKY gene functions to aid further exploration of the functions and regulatory mechanisms of PmWRKY genes in biological and abiotic stress in P. massoniana.

Effects of shading on lignin biosynthesis in the leaf of tea plant (Camellia sinensis (L.) O. Kuntze)

Shading can effectively reduce photoinhibition and improve the quality of tea. Lignin is one of the most important secondary metabolites that play vital functions in plant growth and development. However, little is known about the relationship between shading and xylogenesis in tea plant. To investigate the effects of shading on lignin accumulation in tea plants, 'Longjing 43' was treated with no shading (S0), 40% (S1) and 80% (S2) shading treatments, respectively. The leaf area and lignin content of tea plant leaves decreased under shading treatments (especially S2). The anatomical characteristics showed that lignin is mainly distributed in the xylem of tea leaves. Promoter analysis indicated that the genes involved in lignin pathway contain several light recognition elements. The transcript abundances of 12 lignin-associated genes were altered under shading treatments. Correlation analysis indicated that most genes showed strong positive correlation with lignin content, and CsPAL, Cs4CL, CsF5H, and CsLAC exhibited significant positively correlation under 40% and 80% shading treatments. The results showed that shading may have an important effect on lignin accumulation in tea leaves. This work will potentially helpful to understand the regulation mechanism of lignin pathway under shading treatment, and provide reference for reducing lignin content and improving tea quality through shading treatment in field operation.

Genome-wide interologous interactome map (TeaGPIN) of Camellia sinensis

Tea, prepared from the young leaves of Camellia sinensis, is a non-alcoholic beverage globally consumed due to its antioxidant properties, strong taste and aroma. Although, the genomic data of this medicinally and commercially important plant is available, studies related to its sub-cellular interactomic maps are less explored. In this work, we propose a genome-wide interologous protein-protein interaction (PPI) network of tea, termed as TeaGPIN, consisting of 12,033 nodes and 216,107 interactions, developed using draft genome of tea and known PPIs exhaustively collected from 49 template plants. TeaGPIN interactions are prioritized using domain-domain interactions along with the interolog information. A high-confidence TeaGPIN consisting of 5983 nodes and 58,867 edges is reported and its interactions are further evaluated using protein co-localization similarities. Based on three network centralities (degree, betweenness and eigenvector), 1302 key proteins are reported in tea to have p-value <0.01 by comparing the TeaGPIN with 10,000 realizations of Erdős-Rényi and Barabási-Albert based corresponding random network models. Functional content of TeaGPIN is assessed using KEGG and GO annotations and its modular architecture is explored. Network based characterization is carried-out on the transcription factors, and proteins involved flavonoid biosynthesis and photosynthesis pathways to find novel candidates involved in various regulatory processes. We believe the proposed TeaGPIN will impart useful insights in understanding various mechanisms related to growth and development as well as defence against biotic and abiotic perturbations.

TeaCoN: a database of gene co-expression network for tea plant (Camellia sinensis)

Background

Tea plant (Camellia sinensis) is one of the world’s most important beverage crops due to its numerous secondary metabolites conferring tea quality and health effects. However, only a small fraction of tea genes (especially for those metabolite-related genes) have been functionally characterized to date. A cohesive bioinformatics platform is thus urgently needed to aid in the functional determination of the remaining genes.

Description

TeaCoN, a database of gene co-expression network for tea plant, was established to provide genome-wide associations in gene co-expression to survey gene modules (i.e., co-expressed gene sets) for a function of interest. TeaCoN featured a comprehensive collection of 261 high-quality RNA-Seq experiments that covered a wide range of tea tissues as well as various treatments for tea plant. In the current version of TeaCoN, 31,968 (94% coverage of the genome) tea gene models were documented. Users can retrieve detailed co-expression information for gene(s) of interest in four aspects: 1) co-expressed genes with the corresponding Pearson correlation coefficients (PCC-values) and statistical P-values, 2) gene information (gene ID, description, symbol, alias, chromosomal location, GO and KEGG annotation), 3) expression profile heatmap of co-expressed genes across seven main tea tissues (e.g., leaf, bud, stem, root), and 4) network visualization of co-expressed genes. We also implemented a gene co-expression analysis, BLAST search function, GO and KEGG enrichment analysis, and genome browser to facilitate use of the database.

Conclusion

The TeaCoN project can serve as a beneficial platform for candidate gene screening and functional exploration of important agronomical traits in tea plant. TeaCoN is freely available at http://teacon.wchoda.com.

Genome-wide investigation of WRKY transcription factors in Tartary buckwheat (Fagopyrum tataricum) and their potential roles in regulating growth and development

BACKGROUND

The WRKY gene family plays important roles in plant biological functions and has been identified in many plant species. With the publication of the Tartary buckwheat genome, the evolutionary characteristics of the WRKY gene family can be systematically explored and the functions of Fagopyrum tataricum WRKY (FtWRKY) genes in the growth and development of this plant also can be predicted.

METHODS

In this study, the FtWRKY genes were identified by the BLASTP method, and HMMER, SMART, Pfam and InterPro were used to determine whether the FtWRKY genes contained conserved domains. The phylogenetic trees including FtWRKY and WRKY genes in other plants were constructed by the neighbor-joining (NJ) and maximum likelihood (ML) methods. The intron and exon structures of the FtWRKY genes were analyzed by the gene structure display server, and the motif compositions were analyzed by MEME. Chromosome location information of FtWRKY genes was obtained with gff files and sequencing files, and visualized by Circos, and the collinear relationship was analyzed by Dual synteny plotter software. The expression levels of 26 FtWRKY genes from different groups in roots, leaves, flowers, stems and fruits at the green fruit, discoloration and initial maturity stage were measured through quantitative real-time polymerase chain reaction (qRT-PCR) analysis.

RESULTS

A total of 76 FtWRKY genes identified from the Tartary buckwheat genome were divided into three groups. FtWRKY genes in the same group had similar gene structures and motif compositions. Despite the lack of tandem-duplicated gene pairs, there were 23 pairs of segmental-duplicated gene pairs. The synteny gene pairs of FtWRKY genes and Glycine max WRKY genes were the most. FtWRKY42 was highly expressed in roots and may perform similar functions as its homologous gene AtWRKY75, playing a role in lateral root and hairy root formation. FtWRKY9, FtWRKY42 and FtWRKY60 were highly expressed in fruits and may play an important role in fruit development.

CONCLUSION

We have identified several candidate FtWRKY genes that may perform critical functions in the development of Tartary buckwheat root and fruit, which need be verified through further research. Our study provides useful information on WRKY genes in regulating growth and development and establishes a foundation for screening WRKY genes to improve Tartary buckwheat quality.

Genome-Wide Identification and Expression Profile Analysis of WRKY Family Genes in the Autopolyploid Saccharum spontaneum

WRKY is one of the largest transcription factor families in plants and plays important roles in the regulation of developmental and physiological processes. To date, the WRKY gene family has not been identified in Saccharum species because of its complex polyploid genome. In this study, a total of 294 sequences for 154 SsWRKY genes were identified in the polyploid Saccharum spontaneum genome and then named on the basis of their chromosome locations, including 13 (8.4%) genes with four alleles, 29 (18.8%) genes with three alleles and 41 (26.6%) genes with two alleles. Among them, 73.8% and 16.0% of the SsWRKY genes originated from segmental duplications and tandem duplications, respectively. The WRKY members exhibited conserved gene structures and amino acid sequences among the allelic haplotypes, which were accompanied by variations in intron sizes. Phylogenetic and collinearity analyses revealed that 27 SsWRKYs originated after the split of sorghum and Saccharum, resulting in a significantly higher number of WRKYs in sugarcane than in the proximal diploid species sorghum. The analysis of RNA-seq data revealed that SsWRKYs' expression profiles in 46 different samples including different developmental stages revealed distinct temporal and spatial patterns with 52 genes expressed in all tissues, four genes not expressed in any tissues and 21 SsWRKY genes likely to be involved in photosynthesis. The comprehensive analysis of SsWRKYs' expression will provide an important and valuable foundation for further investigation of the regulatory mechanisms of WRKYs in physiological roles in sugarcane S. spontaneum.

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.

Identification of MYB Transcription Factors Regulating Theanine Biosynthesis in Tea Plant Using Omics-Based Gene Coexpression Analysis

Theanine (thea) is the most abundant free amino acid in tea plant (Camellia sinensis) and one of the most important secondary metabolites conferring tea quality and health benefits. Great effort has recently been made to functionally dissect enzyme genes (e.g., GS, GDH, GOGAT) responsible for in vivo thea accumulation. However, the transcriptional regulation of its biosynthesis remains to be explored. Starting from publicly available (condition-independent) tea transcriptome data, we performed an exhaustive coexpression analysis between transcription factor (TF) genes and thea enzyme genes in tea plant. Our results showed that two typical plant-specialized (secondary) metabolites related TF families, such as MYB, bHLH, together with WD40 domain proteins, were prominently involved, suggesting a potential MYB-bHLH-WD40 (MBW) complex-mediated regulatory pattern in thea pathway. Aiming at the most involved MYB family, we screened seven MYB genes as thea candidate regulators through a stringent multistep selection (e.g., filtering with condition-specific nitrogen-treated transcriptome data). The control of MYB regulators in thea biosynthesis was further demonstrated using an integrated analysis of thea accumulation and MYB expression in several major tea tissues, including leave, bud, root, and stem. Our investigation aided tea researchers in having a comprehensive view of transcriptional regulatory landscape in thea biosynthesis, serving as the first platform for studying molecular regulation in thea pathway and a paradigm for understanding the characteristic components biosynthesis in nonmodel plants.

Understanding the Effect of Structural Diversity in WRKY Transcription Factors on DNA Binding Efficiency through Molecular Dynamics Simulation

A precise understanding of the molecular mechanism involved in stress conditions has great importance for crop improvement. Biomolecules, such as WRKY proteins, which are the largest transcription factor family that is widely distributed in higher plants, plays a significant role in plant defense response against various biotic and abiotic stressors. In the present study, an extensive homology-based three-dimensional model construction and subsequent interaction study of WRKY DNA-binding domain (DBD) in CcWRKY1 (Type I), CcWRKY51 (Type II), and CcWRKY70 (Type III) belonging to pigeonpea, a highly tolerant crop species, was performed. Evaluation of the generated protein models was done to check their reliability and accuracy based on the quantitative and qualitative parameters. The final model was subjected to investigate the comparative binding analysis of different types of WRKY–DBD with DNA-W-box (a cis-acting element) by protein–DNA docking and molecular dynamics (MD) simulation. The DNA binding specificity with WRKY variants was scrutinized through protein–DNA interaction using the HADDOCK server. The stability, as well as conformational changes of protein–DNA complex, was investigated through molecular dynamics (MD) simulations for 100 ns using GROMACS. Additionally, the comparative stability and dynamic behavior of each residue of the WRKY–DBD type were analyzed in terms of root mean square deviation (RMSD), root mean square fluctuation (RMSF)values of the backbone atoms for each frame taking the minimized structure as a reference. The details of DNA binding activity of three different types of WRKY–DBD provided here will be helpful to better understand the regulation of WRKY gene family members in plants.

Construction and analysis of an interologous protein-protein interaction network of Camellia sinensis leaf (TeaLIPIN) from RNA-Seq data sets

An interologous PPI network of tea leaf is designed by developing reference transcriptome assembly and using experimentally validated PPIs in plants. Key regulatory proteins are proposed and potential TFs are predicted. Worldwide, tea (Camellia sinensis) is the most consumed beverage primarily due to the taste, flavour, and aroma of its newly formed leaves; and has been used as an important ingredient in several traditional medicinal systems because of its antioxidant properties. For this medicinally and commercially important plant, design principles of gene-regulatory and protein-protein interaction (PPI) networks at sub-cellular level are largely un-characterized. In this work, we report a tea leaf interologous PPI network (TeaLIPIN) consisting of 11,208 nodes and 197,820 interactions. A reference transcriptome assembly was first developed from all the 44 samples of 6 publicly available leaf transcriptomes (1,567,288,290 raw reads). By inferring the high-confidence interactions among potential proteins coded by these transcripts using known experimental information about PPIs in 14 plants, an interologous PPI network was constructed and its modular architecture was explored. Comparing this network with 10,000 realizations of two types of corresponding random networks (Erdős-Rényi and Barabási-Albert models) and examining over three network centrality metrics, we predict 2750 bottleneck proteins (having p values < 0.01). 247 of these are deduced to have transcription factor domains by in-house developed HMM models of known plant TFs and these were also mapped to the draft tea genome for searching their probable loci of origin. Co-expression analysis of the TeaLIPIN proteins was also performed and top ranking modules are elaborated. We believe that the proposed novel methodology can easily be adopted to develop and explore the PPI interactomes in other plant species by making use of the available transcriptomic data.

Association of transcription factor WRKY56 gene from Populus simonii × P. nigra with salt tolerance in Arabidopsis thaliana

The WRKY transcription factor family is one of the largest groups of transcription factor in plants, playing important roles in growth, development, and biotic and abiotic stress responses. Many WRKY genes have been cloned from a variety of plant species and their functions have been analyzed. However, the studies on WRKY transcription factors in tree species under abiotic stress are still not well characterized. To understand the effects of the WRKY gene in response to abiotic stress, mRNA abundances of 102 WRKY genes in Populus simonii × P. nigra were identified by RNA sequencing under normal and salt stress conditions. The expression of 23 WRKY genes varied remarkably, in a tissue-specific manner, under salt stress. Since the WRKY56 was one of the genes significantly induced by NaCl treatment, its cDNA fragment containing an open reading frame from P. simonii × P. nigra was then cloned and transferred into Arabidopsis using the floral dip method. Under salt stress, the transgenic Arabidopsis over-expressed the WRKY56 gene, showing an increase in fresh weight, germination rate, proline content, and peroxidase and superoxide dismutase activity, when compared with the wild type. In contrast, transgenic Arabidopsis displayed a decrease in malondialdehyde content under salt stress. Overall, these results indicated that the WRKY56 gene played an important role in regulating salt tolerance in transgenic Arabidopsis.

Understanding the Role of the WRKY Gene Family under Stress Conditions in Pigeonpea (Cajanus Cajan L.)

Pigeonpea (Cajanus cajan L.), a protein-rich legume, is a major food component of the daily diet for residents in semi-arid tropical regions of the word. Pigeonpea is also known for its high level of tolerance against biotic and abiotic stresses. In this regard, understanding the genes involved in stress tolerance has great importance. In the present study, identification, and characterization of WRKY, a large transcription factor gene family involved in numerous biological processes like seed germination, metabolism, plant growth, biotic and abiotic stress responses was performed in pigeonpea. A total of 94 WRKY genes identified in the pigeonpea genome were extensively characterized for gene-structures, localizations, phylogenetic distribution, conserved motif organizations, and functional annotation. Phylogenetic analysis revealed three major groups (I, II, and III) of pigeonpea WRKY genes. Subsequently, expression profiling of 94 CcWRKY genes across different tissues like root, nodule, stem, petiole, petal, sepal, shoot apical meristem (SAM), mature pod, and mature seed retrieved from the available RNAseq data identified tissue-specific WRKY genes with preferential expression in the vegetative and reproductive stages. Gene co-expression networks identified four WRKY genes at the center of maximum interaction which may play a key role in the entire WRKY regulations. Furthermore, quantitative real-time polymerase chain reaction (qRT-PCR) expression analysis of WRKY genes in root and leaf tissue samples from plants under drought and salinity stress identified differentially expressed WRKY genes. The study will be helpful to understand the evolution, regulation, and distribution of the WRKY gene family, and additional exploration for the development of stress tolerance cultivars in pigeonpea and other legumes crops.

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.

Transcriptomic and Metabolic Insights into the Distinctive Effects of Exogenous Melatonin and Gibberellin on Terpenoid Synthesis and Plant Hormone Signal Transduction Pathway in Camellia sinensis

Melatonin and gibberellin are bioactive molecules in plants. In the present study, the role of exogenous melatonin (MT) and gibberellin (GA) in the tea plant was explored by transcriptome and metabolic analysis. Results showed that the growth of tea plant was enhanced by MT treatment. The pathways of terpenoid synthesis and plant-pathogen interaction were significantly strengthened, combined with the upregulation of LRR-RLK and transcription factors which contributed to the growth of tea plant. The internode elongation and leaf enlargement were hastened by GA treatment. Significantly modulated expression occurred in the plant hormonal signal transduction, complemented by the upregulation of phenylpropanoid biosynthesis and expansins to achieve growth acceleration, whereas the flavonoid synthesis was repressed in GA treatment. Therefore, the distinctive effect of MT and GA treatment on tea plant was different. The MT exhibited significant promotion in terpenoid synthesis, especially, TPS14 and TPS1. GA was prominent in coordinated regulation of plant hormonal signal transduction.

Genome-wide Analysis of the WRKY Gene Family and its Response to Abiotic Stress in Buckwheat (Fagopyrum Tataricum)

The WRKY gene family is an ancient plant transcription factor (TF) family with a vital role in plant growth and development, especially in response to biotic and abiotic stresses. Although many researchers have studied WRKY TFs in numerous plant species, little is known of them in Tartary buckwheat (Fagopyrum tataricum). Based on the recently reported genome sequence of Tartary buckwheat, we identified 78 FtWRKY proteins that could be classified into three major groups. All 77 WRKY genes were distributed unevenly across all eight chromosomes. Exon-intron analysis and motif composition prediction revealed the complexity and diversity of FtWRKYs, indicating that WRKY TFs may be of significance in plant growth regulation and stress response. Two separate pairs of tandem duplication genes were found, but no segmental duplications were identified. Overall, most orthologous gene-pairs between Tartary and common buckwheat evolved under strong purifying selection. qRT-PCR was used to analyze differences in expression among four FtWRKYs (FtWRKY6, 74, 31, and 7) under salt, drought, cold, and heat treatments. The results revealed that all four proteins are related to abiotic stress responses, although they exhibited various expression patterns. In particular, the relative expression levels of FtWRKY6, 74, and 31 were significantly upregulated under salt stress, while the highest expression of FtWRKY7 was observed from heat treatment. This study provides comprehensive insights into the WRKY gene family in Tartary buckwheat, and can support the screening of additional candidate genes for further functional characterization of WRKYs under various stresses.

Molecular Characterization of WRKY Transcription Factors That Act as Negative Regulators of O-Methylated Catechin Biosynthesis in Tea Plants ( Camellia sinensis L.)

Tea O-methylated catechins, especially (-)-epigallocatechin 3- O-(3- O-methyl)gallate (EGCG3″Me), have been attracting much attention as a result of their positive health effects. The transcription regulators of O-methylated catechin biosynthesis remain elusive. In this study, the expression pattern of genes related to O-methylated catechin biosynthesis, including CsLAR, CsANS, CsDFR, CsANR, and CCoAOMT, in three tea cultivars with different contents of EGCG3″Me was investigated. Two WRKY transcription factors (TFs), designated as CsWRKY31 and CsWRKY48, belonging to groups IIb and IIc of the WRKY family, respectively, were further identified. CsWRKY31 and CsWRKY48 were nuclear-localized proteins and possessed transcriptional repression ability. Furthermore, expression of CsWRKY31 and CsWRKY48 showed negative correlation with CsLAR, CsDFR, and CCoAOMT during EGCG3″Me accumulation in tea leaves. More importantly, W-box (C/T)TGAC(T/C) elements were located in the promoter of CsLAR, CsDFR, and CCoAOMT, and further assays revealed that CsWRKY31 and CsWRKY48 were capable of repressing the transcription of CsLAR, CsDFR, and CCoAOMT via the attachment of their promoters to the W-box elements. Collectively, our findings identify two novel negative regulators of O-methylated catechin biosynthesis in tea plants, which might provide a potential strategy to breed high-quality tea cultivar.

Unraveling the Roles of Regulatory Genes during Domestication of Cultivated Camellia: Evidence and Insights from Comparative and Evolutionary Genomics

With the increasing power of DNA sequencing, the genomics-based approach is becoming a promising resolution to dissect the molecular mechanism of domestication of complex traits in trees. Genus Camellia possesses rich resources with a substantial value for producing beverage, ornaments, edible oil and more. Currently, a vast number of genetic and genomic research studies in Camellia plants have emerged and provided an unprecedented opportunity to expedite the molecular breeding program. In this paper, we summarize the recent advances of gene expression and genomic resources in Camellia species and focus on identifying genes related to key economic traits such as flower and fruit development and stress tolerances. We investigate the genetic alterations and genomic impacts under different selection programs in closely related species. We discuss future directions of integrating large-scale population and quantitative genetics and multiple omics to identify key candidates to accelerate the breeding process. We propose that future work of exploiting the genomic data can provide insights related to the targets of domestication during breeding and the evolution of natural trait adaptations in genus Camellia.

Identification, characterization and expression analysis of the VQ motif-containing gene family in tea plant (Camellia sinensis)

BACKGROUND

VQ motif-containing (VQ) proteins are plant-specific proteins that interact with WRKY transcription factors and play important roles in plant growth, development and stress response. To date, VQ gene families have been identified and characterized in many plant species, including Arabidopsis, rice and grapevine. However, the VQ gene family in tea plant has not been reported, and the biological functions of this family remain unknown.

RESULTS

In total, 25 CsVQ genes were identified based on the genome and transcriptome of tea plant, and a comprehensive bioinformatics analysis was performed. The CsVQ proteins all contained the typical conserved motif FxxhVQxhTG, and most proteins were localized in the nucleus. The phylogenetic analysis showed that the VQ proteins were classified into 5 groups (I, III-VI); the evolution of the CsVQ proteins is consistent with the evolutionary process of plants, and close proteins shared similar structures and functions. In addition, the expression analysis revealed that the CsVQ genes play important roles in the process of tea plant growth, development and response to salt and drought stress. Furthermore, a potential regulatory network including the interactions of CsVQ proteins with CsWRKY transcription factors and the regulation of upstream microRNA that is closely related to the above-mentioned processes is proposed.

CONCLUSIONS

The results of this study increase our understanding and characterization of CsVQ genes and their encoded proteins in tea plant. This systematic analysis provided comprehensive information for further studies investigating the biological functions of CsVQ proteins in various developmental processes of tea plants.

Genome-wide identification of WRKY family genes and their response to abiotic stresses in tea plant (Camellia sinensis)

The WRKY transcription factors (TFs) family is one of the largest TF families in plants and plays a central role in diverse regulation and multiple stress responses. However, the systematical analysis of the WRKY gene family in tea plant (Camellia sinensis) based on genomic data has been lacking. The primary objective of this study was to set a systematic analysis of the WRKY gene family based on genomic data in tea plant and analyze their expression profiles under various abiotic stresses. We searched the tea plant genome using the consensus model of the WRKY domain (PF03106) and then used these search results to identify all the WRKY family members by SMART and the CDD program. Analyze their phylogeny, classification, structure, conserved motifs, Cis-elements, interactors and expression profiles. 56 putative WRKY genes were identified from the tea plant genome and divided into three main groups (I-III) and five subgroups (IIa-IIe) according to the WRKY domains and the zinc-finger structure. The gene structure and conserved motifs of the CsWRKY genes were also characterized and were consistent with the classification results. Annotation analysis showed that 34 CsWRKY genes may be involved in stress responses. Promoter analysis implied that CsWRKY genes, except for CsWRKY55, possessed at least one abiotic stress response cis-element. Expression profiles of CsWRKY genes in different tissues were analyzed with RNA-seq data. The results showed that 56 CsWRKY genes had differential expression in their transcript abundance. The expression profiles also showed that many identified CsWRKY genes were possibly involved in the response to cold, drought, salt, or ABA treatment. Tea plant genome contains at least 56 WRKY genes. These results provide useful information for further exploring the function and regulatory mechanism of CsWRKY genes in the growth, development, and adaption to abiotic stresses in tea plant.

Genome-Wide Identification, Classification and Expression Analysis of the HSP Gene Superfamily in Tea Plant (Camellia sinensis)

Heat shock proteins (HSPs) function as molecular chaperones. These proteins are encoded by a multigene family whose members play crucial roles in plant growth, development and stress response. However, little is known about the HSP gene superfamily in tea plant. In this study, a total of 47 CsHSP genes were identified, including 7 CsHSP90, 18 CsHSP70, and 22 CssHSP genes. Phylogenetic and composition analyses showed that CsHSP proteins in the same subfamily have similar gene structures and conserved motifs, but significant differences exist in the different subfamilies. In addition, expression analysis revealed that almost all CsHSP genes were specifically expressed in one or more tissues, and significantly induced under heat and drought stress, implying that CsHSP genes play important roles in tea plant growth, development, and response to heat and drought stress. Furthermore, a potential interaction network dominated by CsHSPs, including HSP70/HSP90 organizing protein (HOP) and heat shock transcription factor (HSF), is closely related to the abovementioned processes. These results increase our understanding of CsHSP genes and their roles in tea plant, and thus, this study could contribute to the cloning and functional analysis of CsHSP genes and their encoded proteins in the future.

Genomic and transcriptomic analyses of HD-Zip family transcription factors and their responses to abiotic stress in tea plant (Camellia sinensis)

Tea plant (Camellia sinensis (L.) O. Kuntze) is a perennial evergreen woody plant, and its leaves contain various beneficial ingredients and have healthy efficacy. HD-Zip (homeodomain-leucine zipper) transcription factors (TFs) are widely distributed in plants and play an important role in plant growth and environmental response. To date, knowledge on HD-Zip gene family in tea plant is still limited. In this study, 33 HD-Zip TFs were selected based on the genomic and transcriptomic databases of tea plant. The conserved domains and common motifs of these TFs were predicted and analyzed. These 33 Cshdz TFs were divided into four groups (HD-Zip I, HD-Zip II, HD-Zip III, and HD-Zip IV). The interaction network of the HD-Zip proteins of tea plant was established based on the data of Arabidopsis. In addition, the expression levels of these Cshdz genes in tea plant cv. 'Longjing43' were detected and analyzed under five abiotic stress treatments. Results showed that the different expression profiles of Cshdz genes were associated with different abiotic stress treatments. Our findings suggested a potential relationship between the resistance of tea plant and its Cshdz genes.

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.

Analysis of WRKY transcription factors and characterization of two Botrytis cinerea-responsive LrWRKY genes from Lilium regale

A major constraint in producing lilies is gray mold caused by Botrytis elliptica and B. cinerea. WRKY transcription factors play important roles in plant immune responses. However, limited information is available about the WRKY gene family in lily plants. In this study, 23 LrWRKY genes with complete WRKY domains were identified from the Botrytis-resistant species Lilium regale. The putative WRKY genes were divided into seven subgroups (Group I, IIa-e, and III) according to their structural features. Sequence alignment revealed that LrWRKY proteins have a highly conserved WRKYGQK domain and a variant, the WRKYGKK domain, and these proteins generally contained similar motif compositions throughout the same subgroup. Functional annotation predicted they might be involved in biological processes related to abiotic and biotic stresses. A qRT-PCR analysis confirmed that expression of six LrWRKY genes in L. regale or the susceptible Asian hybrid 'Yale' was induced by B. cinerea infection. Among these genes, LrWRKY4, LrWRKY8 and LrWRKY10 were expressed at a higher level in L. regale than 'Yale', while the expression of LrWRKY6 and LrWRKY12 was lower in L. regale. Furthermore, LrWRKY4 and LrWRKY12 genes, which also respond to salicylic acid (SA) and methyl jasmonate (MeJA) treatments, were isolated from L. regale. Subcellular localization analysis determined that they were targeted to the nucleus. Constitutive expression of LrWRKY4 and LrWRKY12 in Arabidopsis resulted in plants that were more resistant to B. cinerea than wild-type plants. This resistance was coupled with the transcriptional changes of SA and JA-responsive genes. Overall, our study provides valuable information about the structural and functional characterization of LrWRKY genes that will not only deepen our understanding of the molecular mechanisms underlying the defense of lily against B. cinerea but also offer potential targets for cultivar improvement via biotechnology.

Genome-wide identification and expression analysis of GRAS family transcription factors in tea plant (Camellia sinensis)

GRAS proteins are important transcription factors that play multifarious roles in regulating the growth and development as well as stress responses of plants. Tea plant is an economically important leaf -type beverage crop. Information concerning GRAS family transcription factors in tea plant is insufficient. In this study, 52 CsGRAS genes encoding GRAS proteins were identified from tea plant genome database. Phylogenetic analysis of the identified GRAS proteins from tea plant, Arabidopsis, and rice divided these proteins into at least 13 subgroups. Conserved motif analysis revealed that the gene structure and motif compositions of the proteins were considerably conserved among the same subgroup. Functional divergence analysis indicated that the shifted evolutionary rate might act as a major evolutionary force driving subfamily-specific functional diversification. Transcriptome analysis showed that the transcriptional levels of CsGRAS genes under non-stress conditions varied among different tea plant cultivars. qRT-PCR analysis revealed tissue and development stage-specific expression patterns of CsGRAS genes in tea plant. The expression patterns of CsGRAS genes in response to abiotic stresses and gibberellin treatment suggested the possible multiple functions of these genes. This study provides insights into the potential functions of GRAS genes.

Genome-wide identification of WRKY transcription factors in kiwifruit (Actinidia spp.) and analysis of WRKY expression in responses to biotic and abiotic stresses

As one of the largest transcriptional factor families in plants, WRKY transcription factors play important roles in various biotic and abiotic stress responses. To date, WRKY genes in kiwifruit (Actinidia spp.) remain poorly understood. In our study, o total of 97 AcWRKY genes have been identified in the kiwifruit genome. An overview of these AcWRKY genes is analyzed, including the phylogenetic relationships, exon-intron structures, synteny and expression profiles. The 97 AcWRKY genes were divided into three groups based on the conserved WRKY domain. Synteny analysis indicated that segmental duplication events contributed to the expansion of the kiwifruit AcWRKY family. In addition, the synteny analysis between kiwifruit and Arabidopsis suggested that some of the AcWRKY genes were derived from common ancestors before the divergence of these two species. Conserved motifs outside the AcWRKY domain may reflect their functional conservation. Genome-wide segmental and tandem duplication were found, which may contribute to the expansion of AcWRKY genes. Furthermore, the analysis of selected AcWRKY genes showed a variety of expression patterns in five different organs as well as during biotic and abiotic stresses. The genome-wide identification and characterization of kiwifruit WRKY transcription factors provides insight into the evolutionary history and is a useful resource for further functional analyses of kiwifruit.

Brassinosteroids Attenuate Moderate High Temperature-Caused Decline in Tea Quality by Enhancing Theanine Biosynthesis in Camellia sinensis L

Temperature is a major environmental signal that governs plant growth and development. A moderately high ambient temperature alters plant metabolism without significant induction of heat-stress responses. Despite ancillary reports on the negative effect of warmer climate on tea quality, information on specific effect of sub high temperature (SHT) on theanine accumulation is scanty. L-Theanine is the most abundant free amino acid in tea (Camellia sinensis L.) leaves that contributes to the unique umami flavor of green tea infusion. Tea harvested in warmer months lacks distinctive umami taste due to low theanine content. In this study, we showed that SHT (35°C) gradually decreased theanine concentration over time, which was closely associated with the SHT-induced suppression in theanine biosynthetic genes. 24-epibrassinolide (BR), a bioactive brassinosteroids, attenuated the SHT-induced reduction in theanine concentration by upregulating the transcript levels of theanine biosynthetic genes, such as ARGININE DECARBOXYLASE (CsADC), GLUTAMINE SYNTHETASE (CsGS), GLUTAMATE SYNTHASE (CsGOGAT) and THEANINE SYNTHASE (CsTS). Furthermore, time-course analysis of the activity of theanine biosynthetic enzyme reveals that BR-induced regulation of GS and GOGAT activity plays essential role in maintaining theanine content in tea leaves under SHT, which is consistent with the central position of GOGAT in theanine biosynthetic pathway. Therefore, it is convincing to propose that exogenous BR treatment can be advocated to improve summer tea quality by enhancing in vivo accumulation of theanine. However, a future challenge is to use this information on the role of BR in theanine biosynthesis and thermotolerance to further understand how BR may be tuned to benefit plant fitness for enhancing tea quality.

Genome-wide analysis of WRKY gene family in the sesame genome and identification of the WRKY genes involved in responses to abiotic stresses

BACKGROUND

Sesame (Sesamum indicum L.) is one of the world's most important oil crops. However, it is susceptible to abiotic stresses in general, and to waterlogging and drought stresses in particular. The molecular mechanisms of abiotic stress tolerance in sesame have not yet been elucidated. The WRKY domain transcription factors play significant roles in plant growth, development, and responses to stresses. However, little is known about the number, location, structure, molecular phylogenetics, and expression of the WRKY genes in sesame.

RESULTS

We performed a comprehensive study of the WRKY gene family in sesame and identified 71 SiWRKYs. In total, 65 of these genes were mapped to 15 linkage groups within the sesame genome. A phylogenetic analysis was performed using a related species (Arabidopsis thaliana) to investigate the evolution of the sesame WRKY genes. Tissue expression profiles of the WRKY genes demonstrated that six SiWRKY genes were highly expressed in all organs, suggesting that these genes may be important for plant growth and organ development in sesame. Analysis of the SiWRKY gene expression patterns revealed that 33 and 26 SiWRKYs respond strongly to waterlogging and drought stresses, respectively. Changes in the expression of 12 SiWRKY genes were observed at different times after the waterlogging and drought treatments had begun, demonstrating that sesame gene expression patterns vary in response to abiotic stresses.

CONCLUSIONS

In this study, we analyzed the WRKY family of transcription factors encoded by the sesame genome. Insight was gained into the classification, evolution, and function of the SiWRKY genes, revealing their putative roles in a variety of tissues. Responses to abiotic stresses in different sesame cultivars were also investigated. The results of our study provide a better understanding of the structures and functions of sesame WRKY genes and suggest that manipulating these WRKYs could enhance resistance to waterlogging and drought.

Transcriptome-Wide Identification and Expression Analysis of the NAC Gene Family in Tea Plant [Camellia sinensis (L.) O. Kuntze]

In plants, the NAC (NAM-ATAF1/2-CUC) family of proteins constitutes several transcription factors and plays vital roles in diverse biological processes, such as growth, development, and adaption to adverse factors. Tea, as a non-alcoholic drink, is known for its bioactive ingredients and health efficacy. Currently, knowledge about NAC gene family in tea plant remains very limited. In this study, a total of 45 CsNAC genes encoding NAC proteins including three membrane-bound members were identified in tea plant through transcriptome analysis. CsNAC factors and Arabidopsis counterparts were clustered into 17 subgroups after phylogenetic analysis. Conserved motif analysis revealed that CsNAC proteins with a close evolutionary relationship possessed uniform or similar motif compositions. The distribution of NAC family MTFs (membrane-associated transcription factors) among higher plants of whose genome-wide has been completed revealed that the existence of doubled TMs (transmembrane motifs) may be specific to fabids. Transcriptome analysis exhibited the expression profiles of CsNAC genes in different tea plant cultivars under non-stress conditions. Nine CsNAC genes, including the predicted stress-related and membrane-bound genes, were examined through qRT-PCR (quantitative real time polymerase chain reaction) in two tea plant cultivars, namely, 'Huangjinya' and 'Yingshuang'. The expression patterns of these genes were investigated in different tissues (root, stem, mature leaf, young leaf and bud) and under diverse environmental stresses (drought, salt, heat, cold and abscisic acid). Several CsNAC genes, including CsNAC17 and CsNAC30 that are highly orthologous to known stress-responsive ANAC072/RD26 were identified as highly responsive to abiotic stress. This study provides a global survey of tea plant NAC proteins, and would be helpful for the improvement of stress resistance in tea plant via genetic engineering.

Members of WRKY Group III transcription factors are important in TYLCV defense signaling pathway in tomato (Solanum lycopersicum)

Background

Transmitted by the whitefly Bemisia tabaci, tomato yellow leaf curly virus (TYLCV) has posed serious threats to plant growth and development. Plant innate immune systems against various threats involve WRKY Group III transcription factors (TFs). This group participates as a major component of biological processes in plants.

Results

In this study, 6 WRKY Group III TFs (SolyWRKY41, SolyWRKY42, SolyWRKY53, SolyWRKY54, SolyWRKY80, and SolyWRKY81) were identified, and these TFs responded to TYLCV infection. Subcellular localization analysis indicated that SolyWRKY41 and SolyWRKY54 were nuclear proteins in vivo. Many elements, including W-box, were found in the promoter region of Group III TFs. Interaction network analysis revealed that Group III TFs could interact with other proteins, such as mitogen-activated protein kinase 5 (MAPK) and isochorismate synthase (ICS), to respond to biotic and abiotic stresses. Positive and negative expression patterns showed that WRKY Group III genes could also respond to TYLCV infection in tomato. The DNA content of TYLCV resistant lines after SolyWRKY41 and SolyWRKY54 were subjected to virus-induced gene silencing (VIGS) was lower than that of the control lines.

Conclusions

In the present study, 6 WRKY Group III TFs in tomato were identified to respond to TYLCV infection. Quantitative real-time–polymerase chain reaction (RT-qPCR) and VIGS analyses demonstrated that Group III genes served as positive and negative regulators in tomato–TYLCV interaction. WRKY Group III TFs could interact with other proteins by binding to cis elements existing in the promoter regions of other genes to regulate pathogen-related gene expression.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-016-3123-2) contains supplementary material, which is available to authorized users.