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

Li, Yán; Li, Xiang; Wei, June; Cai, Kewei; Zhang, Hongzhi; Ge, Lili; Ren, Zengjun; Zhao, Chunli; Zhao, Xiyang

doi:10.3390/genes12121867

Cited by 19 publications

(20 citation statements)

References 79 publications

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“…Among SsWRKYs , 22 SsWRKY genes were expressed in the roots ( Figure 7 ). These results concur with research reported for other species, such as A. thaliana [ 46 ], A. truncatum [ 19 ], and C. sativus [ 26 ]. It may be that roots, as an important organ for absorbing water and nutrients, respond first to stress when a plant is subjected to drought, high salt, or other stresses.…”

Section: Discussionsupporting

confidence: 92%

“…In Polygonatum odoratum , expression of PoWRKY1 is induced by cold and drought stress, and overexpression in A. thaliana improved seed germination vigor and root growth of transgenic plants under cold stress and drought [ 18 ]. At least 15 WRKY genes in Acer truncatum are expressed in cold stress [ 19 ]. Furthermore, WRKY40-D and WRKY42-B from Taraxacum antungense have been demonstrated to promote initiation of leaf senescence by promoting the jasmonic acid biosynthesis pathway [ 20 , 21 ].…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Identification and Expression Analysis of WRKY Transcription Factors in Siraitia siamensis

Chen

Shao

et al. 2023

Plants

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WRKY transcription factors, as the largest gene family in higher plants, play an important role in various biological processes including growth and development, regulation of secondary metabolites, and stress response. In this study, we performed genome-wide identification and analysis of WRKY transcription factors in S. siamensis. A total of 59 SsWRKY genes were identified that were distributed on all 14 chromosomes, and these were classified into three major groups based on phylogenetic relationships. Each of these groups had similar conserved motifs and gene structures. We compared all the S. siamensis SsWRKY genes with WRKY genes identified from three diverse plant species, and the results implied that segmental duplication and tandem duplication play an important roles in the evolution processes of the WRKY gene family. Promoter region analysis revealed that SsWRKY genes included many cis-acting elements related to plant growth and development, phytohormone response, and both abiotic and biotic stress. Expression profiles originating from the transcriptome database showed expression patterns of these SsWRKY genes in four different tissues and revealed that most genes are expressed in plant roots. Fifteen SsWRKY genes with low-temperature response motifs were surveyed for their gene expression under cold stress, showing that most genes displayed continuous up-regulation during cold treatment. Our study provides a foundation for further study on the function and regulatory mechanism of the SsWRKY gene family.

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Section: Discussionsupporting

confidence: 92%

Section: Introductionmentioning

confidence: 99%

Genome-Wide Identification and Expression Analysis of WRKY Transcription Factors in Siraitia siamensis

Chen

Shao

et al. 2023

Plants

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“…WRKY domain sequence [13], obtained from the Pfam database (PF03106) (http://pfam. xfam.org/family/PF03106 accessed on 17 July 2022), was used to identify and download WRKY TFs gene members in C. reticulata genome from the Citrus Genome Database (CGD) (https://www.citrusgenomedb.org/ accessed on 18 July 2022) [29] using the BLAST-P (Protein-Basic Local Alignment Search Technique) algorithm.…”

Section: Database Search Classification and Retrieval Of Sequencesmentioning

confidence: 99%

“…WRKY protein directly binds to its associated cis-acting element, the W box (TTGACC/T), and regulates the cold tolerance in plant responses to abiotic stress. When plants are exposed to cold, their gene expressions are changed [13]. Many plant species have already been identified and characterized with the WRKY gene family (Table 1) due to their complicated functions in plant growth and development (both Angiosperms and Gymnosperms) [14].…”

Section: Introductionmentioning

confidence: 99%

Genome Identification and Characterization of WRKY Transcription Factor Gene Family in Mandarin (Citrus reticulata)

Maheen,

Shafiq,

Sadiq

et al. 2023

Agriculture

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WRKY proteins are an important group of transcription factors (TFs) gene family and were identified primarily in plants. WRKY TFs play vital roles in modulating gene expression when plants face detrimental effects due to the environment. In the current study, we focused on using the mandarin citrus (Citrus reticulata) genome to understand the impact of the WRKY gene family on the extraction of alleles mining in mandarins. The mining of the C. reticulata genome identified 46 CrWRKY genes that were classified into three main groups (G1, G2, and G3) further with five subclasses (IIa, IIb, IIc, Iid, and IIe) in the G2 group, and all were presented on 29 scaffolds representing numerous segmental duplications of 100% events established. Multiple sequence analysis predicted the presence of the “WRKYGQK” domain and metal-chelating zinc-finger motif C2H2 in 45 genes, while the “WRKYGQK” domain was replaced with “WRKYGKK” only in CrWRKY20. The comparative relationship of CrWRKY with other plant species using dual synteny analysis revealed that the divergence between C. reticulata and C. grandis occurred after the evolutionary divergence of C. clementine, C. sinensis, C. medica, and C. ichangensis. The possible functions of the CrWRKY genes in mitigating environmental effects were predicted using cis-regulatory elements analysis and in silico RNAseq analysis, for the development of plants. These results provide a robust platform and absence of knowledge for the functional identification from key genes of CrWRKY genes in the mandarin for the possible use to improve key desirable agronomic and consumer-driven fruit quality traits in mandarins and related species.

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“…The diversity of gene structures of the WRKY family implies the diversity of their functions. To date, the WRKY family has been functionally and physiologically characterized in several ornamental plants, such as Dendrobium officinale (Wang et al 2018 ), Acer truncatum (Li et al 2021a ), Prunus mume (Bao et al 2019 ). However, WRKY family has not been described in weeping forsythia.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide investigation of the WRKY transcription factor gene family in weeping forsythia: expression profile and cold and drought stress responses

et al. 2023

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Weeping forsythia is a wide-spread shrub in China with important ornamental, medicinal and ecological values. It is widely distributed in China's warm temperate zone. In plants, WRKY transcription factors play important regulatory roles in seed germination, flower development, fruit ripening and coloring, and biotic and abiotic stress response. To date, WRKY transcription factors have not been systematically studied in weeping forsythia. In this study, we identified 79 WRKY genes in weeping forsythia and classified them according to their naming rules in Arabidopsis thaliana. Phylogenetic tree analysis showed that, except for IIe subfamily, whose clustering was inconsistent with A. thaliana clustering, other subfamily clustering groups were consistent. Cis-element analysis showed that WRKY genes related to pathogen resistance in weeping forsythia might be related to methyl jasmonate and salicylic acid-mediated signaling pathways. Combining cis-element and expression pattern analyses of WRKY genes showed that more than half of WRKY genes were involved in light-dependent development and morphogenesis in different tissues. The gene expression results showed that 13 WRKY genes were involved in drought response, most of which might be related to the abscisic acid signaling pathway, and a few of which might be regulated by MYB transcription factors. The gene expression results under cold stress showed that 17 WRKY genes were involved in low temperature response, and 9 of them had low temperature responsiveness cis-elements. Our study of WRKY family in weeping forsythia provided useful resources for molecular breeding and important clues for their functional verification.

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

Cited by 19 publications

References 79 publications

Genome-Wide Identification and Expression Analysis of WRKY Transcription Factors in Siraitia siamensis

Genome-Wide Identification and Expression Analysis of WRKY Transcription Factors in Siraitia siamensis

Genome Identification and Characterization of WRKY Transcription Factor Gene Family in Mandarin (Citrus reticulata)

Genome-wide investigation of the WRKY transcription factor gene family in weeping forsythia: expression profile and cold and drought stress responses

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