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

Ren, Liping; Wenyang, Wan; Yin, Da‐Chuan; Deng, Xianhui; Ma, Zongxin; Gao, Ting; Xiaohan, Cao

doi:10.3389/fpls.2022.1063850

Cited by 6 publications

(2 citation statements)

References 88 publications

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“…As the first enzyme of the MEP pathway, 1-deoxyxylose-5-phosphate synthetase (DXS) is a rate-limiting enzyme of this pathway, which plays a key role in regulating the synthesis of terpenoids [32]. WRKY is a class of DNA-specific binding transcription factors that regulate metabolic processes by binding promoter elements of key enzyme genes in the plant secondary metabolic biosynthesis pathway [33]. The reference genes identified through this study will facilitate the future gene function analysis in C. burmannii.…”

Section: Introductionmentioning

confidence: 99%

Reference Genes Selection and Validation for Cinnamomum burmanni by Real-Time Quantitative Polymerase Chain Reaction

Shi,

Cai,

Yao

et al. 2024

IJMS

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In recent years, the field of biology has witnessed a surge of interest in genomics research due to the advancements in biotechnology. Gene expression pattern analysis plays a crucial role in this research, as it enables us to understand the regulatory mechanism of gene expression and the associated biological processes. Real-time quantitative polymerase chain reaction (q-PCR) is an efficient method to analyze the gene expression patterns, for which accuracy relies on the standardized analysis of reference genes. However, numerous studies have shown that no reference gene is universal in all conditions, so screening a suitable reference gene under certain conditions is of great importance. Cinnamomum burmannii (C. burmannii) is rich in volatile components and has high medicinal and economic value. However, knowledge of the screening of reference genes for the gene expression analysis of C. burmannii is insufficient. Aiming at this problem, we evaluated and screened the reference genes in C. burmannii under different experimental conditions, including different abiotic stresses (Cold-treated, PEG-treated and Nacl-treated), different tissues, leaves at different developmental stages and different chemical types. In this study, different algorithms (∆Ct, geNorm, NormFinder and BestKeeper) were used to evaluate the stability of the candidate reference genes, and RefFinder further merged the output data to screen out the optimum reference gene under various experimental conditions in C. burmannii. The results showed that the optimal reference gene number for gene standardization was 2 under different experimental conditions. RPL27|RPS15 was the most suitable combination under the Nacl-treated and PEG-treated samples. RPL27|APT was the optimum combination under the Cold-treated samples. The optimal combinations of other samples were EF1α|ACT7 for different tissues, eIF-5A|Gllα for different borneol clones in C. burmannii, RPS15|ACT7 for leaves at different developmental stages and RPS15|TATA for all samples. Additionally, two terpenoid synthesis-related genes (CbWRKY4 and CbDXS2) were standardized to verify the feasibility of the selected reference genes under different experimental conditions. This study will be helpful for the subsequent molecular genetic mechanism study of C. burmannii.

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Section: Introductionmentioning

confidence: 99%

Reference Genes Selection and Validation for Cinnamomum burmanni by Real-Time Quantitative Polymerase Chain Reaction

Shi,

Cai,

Yao

et al. 2024

IJMS

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“…Group 3 proteins also have one WRKY domain, but the structure of zinc-finger is C2-H-C ( Ning et al., 2017 ). With the release of many plant genomes, whole-genome identification of WRKY genes has been reported in many plant species, and the number of WRKY family members in a species varies from dozens to hundreds ( He et al., 2016 ; Liu et al., 2017 ; Karkute et al., 2018 ; Li et al., 2018 ; Chen et al., 2020 ; Wei et al., 2022 ; Zhang et al., 2022 ; Pan et al., 2023 ; Ren et al., 2023 ).…”

Section: Introductionmentioning

confidence: 99%

Comprehensive analysis of the WRKY gene family in Cucumis metuliferus and their expression profile in response to an early stage of root knot nematode infection

Ling

Hao

et al. 2023

Front. Plant Sci.

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Root-knot nematode (RKN) is a major factor that limits the growth and productivity of important Cucumis crops, such as cucumber and melon, which lack RKN-resistance genes in their genome. Cucumis metuliferus is a wild Cucumis species that displays a high degree of RKN-resistance. WRKY transcription factors were involved in plant response to biotic stresses. However, little is known on the function of WRKY genes in response to RKN infection in Cucumis crops. In this study, Cucumis metuliferus 60 WRKY genes (CmWRKY) were identified in the C. metuliferus genome, and their conserved domains were classified into three main groups based on multiple sequence alignment and phylogenetic analysis. Synteny analysis indicated that the WRKY genes were highly conserved in Cucumis crops. Transcriptome data from of C. metuliferus roots inoculated with RKN revealed that 16 CmWRKY genes showed differential expression, of which 13 genes were upregulated and three genes were downregulated, indicating that these CmWRKY genes are important to C. metuliferus response to RKN infection. Two differentially expression CmWRKY genes (CmWRKY10 and CmWRKY28) were selected for further functional analysis. Both CmWRKY genes were localized in nucleus, indicating they may play roles in transcriptional regulation. This study provides a foundation for further research on the function of CmWRKY genes in RKN stress resistance and elucidation of the regulatory mechanism.

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Understanding the role of GsWRKY transcription factors modulating the biosynthesis of schaftoside in Grona styracifolia

Yu,

Wang,

Shi

et al. 2023

HORTIC. ADV.

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WRKY transcription factors are pivotal regulators in various aspects of plant biology, including growth, development, secondary metabolic biosynthesis, and responses to both biotic and abiotic stresses. The legume plant Grona styracifolia is widely utilized for its medicinal properties in treating urinary calculi and combating SARS-CoV-2, owing to its bioactive component schaftoside. However, the regulatory function of GsWRKYs in schaftoside biosynthesis within G. styracifolia remains elusive. In the G. styracifolia genome, we identified a total of 102 GsWRKYs, classified phylogenetically into Group I (18), II (68), and III (16). Genomic analysis revealed an uneven distribution of GsWRKYs on chromosomes (Chr), with prevalence on Chr 1, followed by Chr 2, 3, 5, and 6. Among the 82 duplicated GsWRKYs, comprising 12, 54, and 16 members in Group I, II, and III respectively, 11 GsWRKYs were tandemly duplicated genes located across Chr 2 (2), Chr 5 (7), and Chr 9 (2). Weighted gene co-expression network analysis unveiled that 2 Group I (GsWRKY44 and GsWRKY95) and 14 Group II GsWRKYs, including two pairs of segmentally duplicated Group II GsWRKYs associated with thermomorphogenesis, exhibited coexpression with Gronastyracifolia C-glycosyltransferases (GsCGT), a gene encoding a C-glucosyltransferase involved in schaftoside biosynthesis. Furthermore, GsWRKY95 demonstrated coexpression with other schaftoside biosynthetic genes. Dual-luciferase and yeast one-hybrid assays provided additional evidence that GsWRKY95 binds to the W-box of GsCGT, activating its expression. In addition, GsWRKY95- and GsCGT-coexpressing Gronastyracifoliachalcone synthase (GsCHSs), along with 11 pairs of segmentally duplicated Group II GsWRKYs, responded to both abiotic and biotic stresses. Notably, certain GsWRKYs were identified as regulators specific to schaftoside biosynthesis in stems, roots, and leaves. These findings suggest that duplication events, particularly in segmentally duplicated Group II GsWRKYs, play a pivotal role in orchestrating the hierarchical regulation of schaftoside biosynthesis. Overall, our results establish a foundation for genetically enhancing G. styracifolia to abundantly produce schaftoside, thereby contributing to its medicinal efficacy.

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

Cited by 6 publications

References 88 publications

Reference Genes Selection and Validation for Cinnamomum burmanni by Real-Time Quantitative Polymerase Chain Reaction

Reference Genes Selection and Validation for Cinnamomum burmanni by Real-Time Quantitative Polymerase Chain Reaction

Comprehensive analysis of the WRKY gene family in Cucumis metuliferus and their expression profile in response to an early stage of root knot nematode infection

Understanding the role of GsWRKY transcription factors modulating the biosynthesis of schaftoside in Grona styracifolia

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