Comparative genomic analysis of the WRKY III gene family in populus, grape, arabidopsis and rice

Wang, Yiyi; Lin, Feng; Zhu, Yanfang; Li, Yuan; Yan, Hanwei; Xiang, Yan

doi:10.1186/s13062-015-0076-3

Cited by 93 publications

(77 citation statements)

References 54 publications

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“…In previous studies, microsynteny analysis of several plant species was performed to identify the location of homologous genes (Li et al, 2014; Lin et al, 2014; Wang et al, 2015; Cao et al, 2016b). In our research, microsynteny was investigated to infer the relationship of the GRF genes between eudicots (pear, Populus , grape and Arabidopsis ) and monocots (rice).…”

Section: Resultsmentioning

confidence: 99%

Comparative Genomic Analysis of the GRF Genes in Chinese Pear (Pyrus bretschneideri Rehd), Poplar (Populous), Grape (Vitis vinifera), Arabidopsis and Rice (Oryza sativa)

et al. 2016

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Growth-regulating factors (GRFs) are plant-specific transcription factors that have important functions in regulating plant growth and development. Previous studies on GRF family members focused either on a single or a small set of genes. Here, a comparative genomic analysis of the GRF gene family was performed in poplar (a model tree species), Arabidopsis (a model plant for annual herbaceous dicots), grape (one model plant for perennial dicots), rice (a model plant for monocots) and Chinese pear (one of the economical fruit crops). In total, 58 GRF genes were identified, 12 genes in rice (Oryza sativa), 8 genes in grape (Vitis vinifera), 9 genes in Arabidopsis thaliana, 19 genes in poplar (Populus trichocarpa) and 10 genes in Chinese pear (Pyrus bretschneideri). The GRF genes were divided into five subfamilies based on the phylogenetic analysis, which was supported by their structural analysis. Furthermore, microsynteny analysis indicated that highly conserved regions of microsynteny were identified in all of the five species tested. And Ka/Ks analysis revealed that purifying selection plays an important role in the maintenance of GRF genes. Our results provide basic information on GRF genes in five plant species and lay the foundation for future research on the functions of these genes.

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Section: Resultsmentioning

confidence: 99%

Comparative Genomic Analysis of the GRF Genes in Chinese Pear (Pyrus bretschneideri Rehd), Poplar (Populous), Grape (Vitis vinifera), Arabidopsis and Rice (Oryza sativa)

et al. 2016

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“…The variation in the number of group III WRKY genes was considered to be one of the causes of diversity of WRKY gene family size [52]. In C. canephora, five group III CcWRKY genes were fewer than S. lycopersicum, A. thaliana, G. max, and similar to V. vinifera and C. papaya (Figure 1).…”

Section: Phylogenetic Analysis Conserved Motifs and Structure Of Thmentioning

confidence: 99%

Genome-Wide Identification of WRKY Genes and Their Response to Cold Stress in Coffea canephora

Dong

Yang

Zhang

et al. 2019

Forests

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WRKY transcription factors are known to play roles in diverse stress responses in plants. Low temperatures limit the geographic distribution of Coffea canephora Pierre ex A.Froehner. The WRKYs of C. canephora are still not well characterized, and the response of C. canephora WRKYs (CcWRKYs) under cold stress is still largely unknown. We identified 49 CcWRKYs from the C. canephora genome to gain insight into these mechanisms. These CcWRKYs were divided into three groups that were based on the conserved WRKY domains and zinc-finger structure. Gene expression analysis demonstrated that 14 CcWRKYs were induced during the cold acclimation stage, 17 CcWRKYs were preferentially upregulated by 4 °C treatment, and 12 CcWRKYs were downregulated by cold stress. Subsequently, we carried out a genome-wide analysis to predict 14,513 potential CcWRKY target genes in C. canephora. These isolated genes were involved in multiple biological processes, and most of them could be grouped by the response to stimulus. Among the putative CcWRKY target genes, 235 genes were categorized into response to the cold process, including carbohydrate metabolic, lipid metabolic, and photosynthesis process-related genes. Furthermore, the qRT-PCR and correlation analysis indicated that CcWRKY might control their putative targets that respond to cold stress. These results provide a basis for understanding the molecular mechanism for CcWRKY-mediated cold responses.

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“…It has been reported that WRKY genes from group III play an important role in plant adaptation and evolution [23]. In order to explore how the WRKY group III gene family evolved, a phylogenetic tree of WRKY group III proteins from sunflower with two dicots (Arabidopsis, grape) and two monocots (rice, maize) was constructed, which divided the 17 group III HaWRKYs into three clades.…”

Section: Discussionmentioning

confidence: 99%

“…Profiles of HaWRKY genes under abiotic and biotic stress23 HaWRKY genes which were highly induced in different tissues of common sunflower (except in pollen) were selected to test the reactions of different WRKY genes to different abiotic stresses. response to PEG, among them HaWRKY22/29/74 were significantly downregulated only at high concentration of PEG.…”

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

Chong

Islam

et al. 2020

Preprint

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Background: WRKY transcription factors play important roles in various physiological processes and stress responses in flowering plants. However, the information about WRKY genes in Helianthus annuus L. (common sunflower) is limited. Results: Ninety WRKY (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 and HaWRKY genes within same group or subgroup generally showed similar exon-intron structures and motif compositions. The tandem and segmental duplication possibly contributed to the diversity and expansion of HaWRKY gene families. 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. Conclusions: Ninety WRKY (HaWRKY) genes were identified from H. annuus L. and classified into four groups. Structures of HaWRKY proteins and their evolutionary characteristics were also investigated. The characterization of HaWRKY genes and their expression profiles under biotic and abiotic stresses in this study provide a foundation for further functional analyses of these genes and will be beneficial to crop improvement.

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Comparative genomic analysis of the WRKY III gene family in populus, grape, arabidopsis and rice

Cited by 93 publications

References 54 publications

Comparative Genomic Analysis of the GRF Genes in Chinese Pear (Pyrus bretschneideri Rehd), Poplar (Populous), Grape (Vitis vinifera), Arabidopsis and Rice (Oryza sativa)

Comparative Genomic Analysis of the GRF Genes in Chinese Pear (Pyrus bretschneideri Rehd), Poplar (Populous), Grape (Vitis vinifera), Arabidopsis and Rice (Oryza sativa)

Genome-Wide Identification of WRKY Genes and Their Response to Cold Stress in Coffea canephora

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

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