WRKY Gene Family Research Articles

Genome-Wide Identification of Wheat WRKY Gene Family Reveals That TaWRKY75-A Is Referred to Drought and Salt Resistances.

It is well known that WRKY transcription factors play essential roles in plants’ response to diverse stress responses, especially to drought and salt stresses. However, a full comprehensive analysis of this family in wheat is still missing. Here we used in silico analysis and identified 124 WRKY genes, including 294 homeologous copies from a high-quality reference genome of wheat (Triticum aestivum). We also found that the TaWRKY gene family did not undergo gene duplication rather than gene loss during the evolutionary process. The TaWRKY family members displayed different expression profiles under several abiotic stresses, indicating their unique functions in the mediation of particular responses. Furthermore, TaWRKY75-A was highly induced after polyethylene glycol and salt treatments. The ectopic expression of TaWRKY75-A in Arabidopsis enhanced drought and salt tolerance. A comparative transcriptome analysis demonstrated that TaWRKY75-A integrated jasmonic acid biosynthetic pathway and other potential metabolic pathways to increase drought and salt resistances in transgenic Arabidopsis. Our study provides valuable insights into the WRKY family in wheat and will generate a useful genetic resource for improving wheat breeding.

A WRKY Transcription Factor, EjWRKY17, from Eriobotrya japonica Enhances Drought Tolerance in Transgenic Arabidopsis.

The WRKY gene family, which is one of the largest transcription factor (TF) families, plays an important role in numerous aspects of plant growth and development, especially in various stress responses. However, the functional roles of the WRKY gene family in loquat are relatively unknown. In this study, a novel WRKY gene, EjWRKY17, was characterized from Eriobotrya japonica, which was significantly upregulated in leaves by melatonin treatment during drought stress. The EjWRKY17 protein, belonging to group II of the WRKY family, was localized in the nucleus. The results indicated that overexpression of EjWRKY17 increased cotyledon greening and root elongation in transgenic Arabidopsis lines under abscisic acid (ABA) treatment. Meanwhile, overexpression of EjWRKY17 led to enhanced drought tolerance in transgenic lines, which was supported by the lower water loss, limited electrolyte leakage, and lower levels of reactive oxygen species (ROS) and malondialdehyde (MDA). Further investigations showed that overexpression of EjWRKY17 promoted ABA-mediated stomatal closure and remarkably up-regulated ABA biosynthesis and stress-related gene expression in transgenic lines under drought stress. Overall, our findings reveal that EjWRKY17 possibly acts as a positive regulator in ABA-regulated drought tolerance.

Genome-wide identification and expression analysis of the WRKY transcription factor family in flax (Linum usitatissimum L.)

BackgroundMembers of the WRKY protein family, one of the largest transcription factor families in plants, are involved in plant growth and development, signal transduction, senescence, and stress resistance. However, little information is available about WRKY transcription factors in flax (Linum usitatissimum L.).ResultsIn this study, comprehensive genome-wide characterization of the flax WRKY gene family was conducted that led to prediction of 102 LuWRKY genes. Based on bioinformatics-based predictions of structural and phylogenetic features of encoded LuWRKY proteins, 95 LuWRKYs were classified into three main groups (Group I, II, and III); Group II LuWRKYs were further assigned to five subgroups (IIa-e), while seven unique LuWRKYs (LuWRKYs 96–102) could not be assigned to any group. Most LuWRKY proteins within a given subgroup shared similar motif compositions, while a high degree of motif composition variability was apparent between subgroups. Using RNA-seq data, expression patterns of the 102 predicted LuWRKY genes were also investigated. Expression profiling data demonstrated that most genes associated with cellulose, hemicellulose, or lignin content were predominantly expressed in stems, roots, and less in leaves. However, most genes associated with stress responses were predominantly expressed in leaves and exhibited distinctly higher expression levels in developmental stages 1 and 8 than during other stages.ConclusionsUltimately, the present study provides a comprehensive analysis of predicted flax WRKY family genes to guide future investigations to reveal functions of LuWRKY proteins during plant growth, development, and stress responses.

Identification, evolution and expression analysis of WRKY gene family in Eucommia ulmoides

The WRKY transcription factors is one of the largest families of transcription factors (TFs) in plants and involved in multiple biological processes. However, the role of the WRKY family had not been reported in Eucommia ulmoides. In this study, 45 WRKY genes (EuWRKY1-45) with conserved WRKY domain were identified in E. ulmoides and classified into three groups. The group II was further divided into five subgroups based on phylogenetic analysis, and each clade was well supported by the conserved motifs. All the genes were located on 34 different scaffolds respectively. A number of development-, light-, hormone-, and stress-related elements were randomly distributed in the promoter sequences of EuWRKYs. Expression profiles indicated that EuWRKY genes were involved in leaf development, and majority of EuWRKYs genes were highly expressed in leaf buds. Co-expression analysis of WRKYs suggested an intricate interplay of growth-related responses. EuWRKY4 was involved in a complex proteins interaction network. Collectively, our results provide extensive insights into the WRKY gene family, thereby contributing to the screening of additional candidate genes in E. ulmoides.

Expression and splicing dynamics of WRKY family genes along physiological exigencies of tea plant (Camellia sinensis)

Expression and splicing dynamics of WRKY family genes along physiological exigencies of tea plant (Camellia sinensis)

Genome-wide Analysis of WRKY Transcription Factor Family in Melon (Cucumis Melo L.) and Their Response to Powdery Mildew

The WRKY family is a large group of transcription factors found in higher plants; it plays an important role in many aspects of biological processes. However, there is very little information about this family in melon (Cucumis melo L.). In our research, 57 candidate WRKY genes in the melon genome were identified. According to their structural and phylogenetic features, the 57 CmWRKY genes were classified into three groups, I, II, and III, and the group II was further divided into five subgroups. Group I included 11 members that all have two conservative WRKY domains and a C2H2-type zinc finger motif; Group II contains 41 WRKY gene family members, that all have a WRKY domain and a C2H2-type zinc finger motif. Five members that all have a conservative WRKY domain and a C2HC-type zinc finger motif are classified as Group III. The expression of 16 selected melon WRKY genes was detected by quantitative real-time PCR after sprayed with salicylic acid (SA) or powdery mildew infection. qRT-PCR analysis showed that 16 CmWRKY genes exhibited distinct expression patterns upon powdery mildew infection, and the expression levels of nine genes were inhibited, and seven genes were induced. After being sprayed with SA, the expression levels of 11 genes were inhibited, and five genes were induced. The data here provide an important basis for further functional studies of the WRKY gene in melon resistance.

Genome-wide identification and comparative analysis of the WRKY gene family in aquatic plants and their response to abiotic stresses in giant duckweed (Spirodela polyrhiza)

WRKY is one of the largest transcription factor families across higher plant species and is involved in important biological processes and plant responses to various biotic/abiotic stresses. However, only a few investigations on WRKYs have been conducted in aquatic plants. This study first systematically analyzed the gene structure, protein properties, and phylogenetic relationship of 693 WRKYs in nine aquatic and two wetland plants at the genome-wide level. The pattern of WRKY groups in two aquatic ferns provided new evidence for the origin and evolution of WRKY genes. ARE cis-regulatory elements show an unusual high frequency in the promoter region of WRKY genes, indicating the adaptation to the aquatic habitat in aquatic plants. The WRKY gene family experienced a series of gene loss events in aquatic plants, especially group III. Further studies were conducted on the interaction network of SpWRKYs, their target genes, and non-coding RNAs. The expression profile of SpWRKYs under phosphate starvation, cold, and submergence conditions revealed that most SpWRKYs are involved in the response to abiotic stresses. Our investigations lay the foundation for further study on the mechanism of WRKYs responding to abiotic stresses in aquatic plants.

Genome-Wide Identification of WRKY Gene Family and Expression Analysis under Abiotic Stress in Barley

The WRKY gene family consists of transcription factors that are widely distributed in plants and play a key role in plant growth and development, secondary metabolite synthesis, biotic and abiotic stress responses, and other biological processes. In this study, 86 WRKY proteins were identified from the barley genome database using bioinformatics and were found to be distributed unevenly on seven chromosomes. According to the structure and phylogenetic relationships, the proteins could be classified into three groups and seven subgroups. The multiple sequence alignment results showed that WRKY domains had different conserved sites in different groups or subgroups, and some members had a special heptapeptide motif. Protein and gene structure analysis indicated that there were significant differences between the groups in terms of the distribution of WRKY motifs and the number of introns in barley. Tissue expression pattern analysis demonstrated that the transcription levels of most genes exhibited tissue and growth-stage specificity. In addition, the analysis of cis-elements in the promoter region revealed that almost all HvWRKYs had plant hormone or stress response cis-elements, and there were differences in the numbers between groups. Finally, the transcriptional levels of 15 HvWRKY genes under drought, cadmium, or salt stress were analyzed by quantitative real-time PCR. It was found that most of the gene expression levels responded to one or more abiotic stresses. These results provide a foundation for further analysis of the function of WRKY gene family members in abiotic stress.

Identification and expression analysis of the WRKY gene family in Isatis indigotica

The WRKY proteins, which represent one of the largest families of transcriptional regulators in plants, play pivotal roles in regulating multiple processes of growth and development, particularly in diverse stress responses. Isatis indigotica is widely used in Traditional Chinese Medicine and is famous for its use as a dye for the color indigo. However, reports of the WRKY gene family in I. indigotica are limited. In this study, 64 IiWRKY genes encoding proteins with the complete WRKY domain were identified from genome of I. indigotica. Based on their structure and phylogenetic relationships of this gene family in I. indigotica, the IiWRKY genes were classified into three groups: Group I (n=13), Group II (n=35) and Group III (n=16). Sequence alignment revealed that IiWRKY proteins harbored two variants, WRKYRQK and WRKYGKK, of the highly conserved WRKYGQK motif. The number of exons in IiWRKY genes varied from two to 14, with most of IiWRKY genes containing three exons. Investigation of gene duplication demonstrated that 10 and 14 IiWRKY genes were incorporated in tandem and segmental duplication events, respectively. Finally, the expression profiles derived from transcriptome data and quantitative real-time PCR analysis showed distinct expression patterns of these IiWRKY gene in five different organs or in response to four abiotic stresses. Taken together, our results will contribute to functional analysis of IiWRKY genes, and also provide a basis for further clarification of the molecular mechanism of stress responses in this important herb.

Molecular mechanism of WRKY12 in regulating plant development

WRKY transcription factors are one of the largest families of transcription factors in higher plants and involved in regulating multiple and complex growth and development processes in plants. WRKY12 is a typical member of WRKY family. This article summarizes recent research progresses on the regulatory mechanism of WRKY12 in multiple growth and development processes, and analyzes the functional differences between WRKY12 and WRKY13. It provides a useful reference for further studying the molecular mechanism of WRKY12 in plant complex developments. It also provides clearer research ideas and reference strategies for exploring the self-regulation of other WRKY member and the mutual regulatory relationships between different WRKY family genes.

Bioinformatics and Expression Analysis of <i>GmWRKY32</i> Gene in Soybean

WRKY transcription factors are very important transcriptional regulators in the process of plant response to plant growth and abiotic stresses. In this study, the open reading frame (ORF) of soybean GmWRKY32 gene was cloned from the WRKY sequence of soybean genome, which was a polypeptide encoding 300 amino acids. Bioinformatics analysis revealed that the WRKY32 protein contained a highly conserved WRKY domain and belonged to Group III of the WRKY gene family. The homology with Glycine soja GsWRKY70, Cajanus cajan CcWRKY70 and Vigna angularis VaWRKY70 proteins was 85%, 79% and 72%, respectively. In addition, GmWRKY32 , is an insoluble protein, no signal peptide and transmembrane domain. Further analysis of the gene expression pattern under different stress and hormone induction showed that after 12 h of treatment with PEG, high salt stress and JA, the expression of GmWRKY32 was increased by 4.5, 4.2 and 3.2 times than that of control, respectively. After 24 h of ABA induction, the expression level of GmWRKY32 was increased 6-fold compared with that of the control. Conjecture that it is closely related to the resistance of soybean to abiotic stress which would lay a foundation for the family structure and functional research of soybean WRKY transcription factors, and will provide scientific basis for research of soybean resistance and molecular breeding.

Genome-wide identification of WRKY gene family and expression analysis under abiotic stresses in Andrographis paniculata

Genome-wide identification of WRKY gene family and expression analysis under abiotic stresses in Andrographis paniculata

Genome-wide characterization of WRKY gene family in Helianthus annuus L. and their expression profiles under biotic and abiotic stresses

WRKY transcription factors play important roles in various physiological processes and stress responses in flowering plants. Sunflower (Helianthus annuus L.) is one of the important vegetable oil supplies in the world. However, the information about WRKY genes in sunflower is limited. In this study, ninety HaWRKY genes were identified and renamed according to their locations on chromosomes. Further phylogenetic analyses classified them into four main groups including a species-specific WKKY group. Besides, HaWRKY genes within the same group or subgroup generally showed similar exon-intron structures and motif compositions. The gene duplication analysis showed that five pairs of HaWRKY genes (HaWRKY8/9, HaWRKY53/54, HaWRKY65/66, HaWRKY66/67 and HaWRKY71/72) are tandem duplicated and four HaWRKY gene pairs (HaWRKY15/82, HaWRKY25/65, HaWRKY28/55 and HaWRKY50/53) are also identified as segmental duplication events, indicating that these duplication genes were contribute to the diversity and expansion of HaWRKY gene families. The dN/dS ratio of these duplicated gene pairs were also calculated to understand the evolutionary constraints. In addition, synteny analyses of sunflower WRKY genes provided deep insight to the evolution of HaWRKY genes. Transcriptomic and qRT-PCR analyses of HaWRKY genes displayed distinct expression patterns in different plant tissues, as well as under various abiotic and biotic stresses, which provide a foundation for further functional analyses of these genes. Those functional genes related to stress tolerance and quality improvement could be applied in marker assisted breeding of the crop.

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

ABSTRACT 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.

Genome-wide identification and functional characterization of the Camelina sativa WRKY gene family in response to abiotic stress

BackgroundWRKY transcription factors are a superfamily of regulators involved in diverse biological processes and stress responses in plants. However, there is limited knowledge about the WRKY family in camelina (Camelina sativa), an important Brassicaceae oil crop with strong tolerance for various stresses. Here, a genome-wide characterization of WRKY proteins is performed to examine their gene structures, phylogenetics, expression, conserved motif organizations, and functional annotation to identify candidate WRKYs that mediate stress resistance regulation in camelinas.ResultsA total of 242 CsWRKY proteins encoded by 224 gene loci distributed unevenly over the chromosomes were identified, and they were classified into three groups by phylogenetic analysis according to their WRKY domains and zinc finger motifs. The 15 CsWRKY gene loci generated 33 spliced variants. Orthologous WRKY gene pairs were identified, with 173 pairs in the C. sativa and Arabidopsis genomes as well as 282 pairs in the C. sativa and B. napus genomes, respectively. A total of 137 segmental duplication events were observed, but there was no tandem duplication in the camelina genome. Ten major conserved motifs were examined, with WRKYGQK being the most conserved, and several variants were present in many CsWRKYs. Expression analysis revealed that 50% more CsWRKY genes were expressed constitutively, and a set of them displayed tissue-specific expression. Notably, 11 CsWRKY genes exhibited significant expression changes in seedlings under cold, salt, and drought stresses, showing a preferentially inducible expression pattern in response to the stress.ConclusionsThe present article describes a detailed analysis of the CsWRKY gene family and its expression profiles in 12 tissues and under several stress conditions. Segmental duplication is the major force underlying the broad expansion of this gene family, and a strong purifying pressure occurred for CsWRKY proteins during their evolution. CsWRKY proteins play important roles in plant development, with differential functions in different tissues. Exceptionally, eleven CsWRKYs, particularly five alternative spliced isoforms, were found to be the possible key players in mediating plant responses to various stresses. Overall, our results provide a foundation for understanding the roles of CsWRKYs and the precise mechanism through which CsWRKYs regulate high stress resistance as well as the development of stress tolerance cultivars among Cruciferae crops.

Function and Mechanism of WRKY Transcription Factors in Abiotic Stress Responses of Plants.

The WRKY gene family is a plant-specific transcription factor (TF) group, playing important roles in many different response pathways of diverse abiotic stresses (drought, saline, alkali, temperature, and ultraviolet radiation, and so forth). In recent years, many studies have explored the role and mechanism of WRKY family members from model plants to agricultural crops and other species. Abiotic stress adversely affects the growth and development of plants. Thus, a review of WRKY with stress responses is important to increase our understanding of abiotic stress responses in plants. Here, we summarize the structural characteristics and regulatory mechanism of WRKY transcription factors and their responses to abiotic stress. We also discuss current issues and future perspectives of WRKY transcription factor research.

WRKY Transcription Factors in Medicago sativa L.: Genome-Wide Identification and Expression Analysis Under Abiotic Stress.

Alfalfa (Medicago sativa L.) is the most widely cultivated leguminous herb in the world. Its agricultural development has been restricted by various adverse environmental conditions, including water deficiency, high salinity, and low temperature. WRKY transcription factors (TFs) serve important roles in the regulation of plant development and stress responses. Research on the WRKY gene family has been reported for several species, but minimal information is available for alfalfa. In the present study, a total of 107 WRKY genes were identified in alfalfa and divided into 3 main groups. The classification, evolution, conserved motifs, and tissue expression were comprehensively analyzed. Meanwhile, 27 MsWRKY candidate genes that may be involved in abiotic stress were isolated through an analysis of gene expression profiles under different stresses, including cold, abscisic acid, drought, and salt treatments. Additionally, investigation of the cis-elements and potential biological functions of these genes further revealed that MsWRKY TFs may serve important roles in multiple stress resistance in alfalfa. This study provides an important foundation for future cloning and functional studies of WRKY genes in alfalfa.

Identification and expression analysis of the WRKY gene family during different developmental stages in Lycium ruthenicum Murr. fruit.

BackgroundThe WRKY gene family, one of the major transcription factor families in plants, plays crucial regulatory roles in physiological and biological developmental processes, and the adaptation of plants to the environment. However, the systematic study of WRKY structure, expression profiling, and regulatory functions has not been extensively reported in Lycium ruthenicum, although these aspects have been comprehensively studied in most plant species.MethodsIn this study, the WRKY genes were identified from a L. ruthenicum transcriptome database by using bioinformatics. The identification, phylogenetic analysis, zinc-finger structures, and conserved motif prediction were extensively explored. Moreover, the expression levels of 23 selected genes with fragments per kilobase of exons per million mapped reads (FPKM) >5 were assayed during different fruit developmental stages with real-time quantitative polymerase chain reaction (RT-qPCR).ResultsA total of 73 putative WRKY proteins in the L. ruthenicum transcriptome database were identified and examined. Forty-four proteins with the WRKY domain were identified and divided into three major groups with several subgroups, in accordance with those in other plant species. All 44 LrWRKY proteins contained one or two conserved WRKY domains and a zinc-finger structure. Conserved motif prediction revealed conservation of the WRKY DNA-binding domain in L. ruthenicum proteins. The selected LrWRKY genes exhibited discrete expression patterns during different fruit developmental stages. Interestingly, five LrWRKYs (-20, -21, -28, -30, and -31) were expressed remarkably throughout the fruit developmental stages.DiscussionOur results reveal the characteristics of the LrWRKY gene family, thus laying a foundation for further functional analysis of the WRKY family in L. ruthenicum.

The genome of Chinese flowering cherry (Cerasus serrulata) provides new insights into Cerasus species

Cerasus serrulata is a flowering cherry germplasm resource for ornamental purposes. In this work, we present a de novo chromosome-scale genome assembly of C. serrulata by the use of Nanopore and Hi-C sequencing technologies. The assembled C. serrulata genome is 265.40 Mb across 304 contigs and 67 scaffolds, with a contig N50 of 1.56 Mb and a scaffold N50 of 31.12 Mb. It contains 29,094 coding genes, 27,611 (94.90%) of which are annotated in at least one functional database. Synteny analysis indicated that C. serrulata and C. avium have 333 syntenic blocks composed of 14,072 genes. Blocks on chromosome 01 of C. serrulata are distributed on all chromosomes of C. avium, implying that chromosome 01 is the most ancient or active of the chromosomes. The comparative genomic analysis confirmed that C. serrulata has 740 expanded gene families, 1031 contracted gene families, and 228 rapidly evolving gene families. By the use of 656 single-copy orthologs, a phylogenetic tree composed of 10 species was constructed. The present C. serrulata species diverged from Prunus yedoensis ~17.34 million years ago (Mya), while the divergence of C. serrulata and C. avium was estimated to have occurred ∼21.44 Mya. In addition, a total of 148 MADS-box family gene members were identified in C. serrulata, accompanying the loss of the AGL32 subfamily and the expansion of the SVP subfamily. The MYB and WRKY gene families comprising 372 and 66 genes could be divided into seven and eight subfamilies in C. serrulata, respectively, based on clustering analysis. Nine hundred forty-one plant disease-resistance genes (R-genes) were detected by searching C. serrulata within the PRGdb. This research provides high-quality genomic information about C. serrulata as well as insights into the evolutionary history of Cerasus species.

Genome-wide analysis of the WRKY gene family in the cucumber genome and transcriptome-wide identification of WRKY transcription factors that respond to biotic and abiotic stresses

BackgroundCucumber (Cucumis sativus L.) is an economically important vegetable crop species. However, it is susceptible to various abiotic and biotic stresses. WRKY transcription factors play important roles in plant growth and development, particularly in the plant response to biotic and abiotic stresses. However, little is known about the expression pattern of WRKY genes under different stresses in cucumber.ResultsIn the present study, an analysis of the new assembly of the cucumber genome (v3.0) allowed the identification of 61 cucumber WRKY genes. Phylogenetic and synteny analyses were performed using related species to investigate the evolution of the cucumber WRKY genes. The 61 CsWRKYs were classified into three main groups, within which the gene structure and motif compositions were conserved. Tissue expression profiles of the WRKY genes demonstrated that 24 CsWRKY genes showed constitutive expression (FPKM > 1 in all samples), and some WRKY genes showed organ-specific expression, suggesting that these WRKYs might be important for plant growth and organ development in cucumber. Importantly, analysis of the CsWRKY gene expression patterns revealed that five CsWRKY genes strongly responded to both salt and heat stresses, 12 genes were observed to be expressed in response to infection from downy mildew and powdery mildew, and three CsWRKY genes simultaneously responded to all treatments analysed. Some CsWRKY genes were observed to be induced/repressed at different times after abiotic or biotic stress treatment, demonstrating that cucumber WRKY genes might play different roles during different stress responses and that their expression patterns vary in response to stresses.ConclusionsSixty-one WRKY genes were identified in cucumber, and insight into their classification, evolution, and expression patterns was gained in this study. Responses to different abiotic and biotic stresses in cucumber were also investigated. Our results provide a better understanding of the function of CsWRKY genes in improving abiotic and biotic stress resistance in cucumber.