Genome-wide identification and comparative expression analysis reveal a rapid expansion and functional divergence of duplicated genes in the WRKY gene family of cabbage, Brassica oleracea var. capitata

Yao, Qiu-Yang; Xia, Enhua; Liu, Feihu; Gao, Li‐Zhi

doi:10.1016/j.gene.2014.12.005

Cited by 38 publications

(23 citation statements)

References 67 publications

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“…WRKYGKK sequence is the most common variant not only in soybean, also in Solanum lycopersicum (Huang et al, 2012 ), L. japonicus (Song et al, 2014 ), and Brassica oleracea var. capitata (Yao et al, 2015 ). WRKYGKK sequence in tobacco WRKY could bind specifically to WK-box (TTTTCCAC), which was significantly different from the consensus sequence of W-box (van Verk et al, 2008 ).…”

Section: Resultsmentioning

confidence: 99%

Global Analysis of WRKY Genes and Their Response to Dehydration and Salt Stress in Soybean

et al. 2016

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WRKY proteins are plant specific transcription factors involved in various developmental and physiological processes, especially in biotic and abiotic stress resistance. Although previous studies suggested that WRKY proteins in soybean (Glycine max var. Williams 82) involved in both abiotic and biotic stress responses, the global information of WRKY proteins in the latest version of soybean genome (Wm82.a2v1) and their response to dehydration and salt stress have not been reported. In this study, we identified 176 GmWRKY proteins from soybean Wm82.a2v1 genome. These proteins could be classified into three groups, namely group I (32 proteins), group II (120 proteins), and group III (24 proteins). Our results showed that most GmWRKY genes were located on Chromosome 6, while chromosome 11, 12, and 20 contained the least number of this gene family. More GmWRKY genes were distributed on the ends of chromosomes to compare with other regions. The cis-acting elements analysis suggested that GmWRKY genes were transcriptionally regulated upon dehydration and salt stress. RNA-seq data analysis indicated that three GmWRKY genes responded negatively to dehydration, and 12 genes positively responded to salt stress at 1, 6, and 12 h, respectively. We confirmed by qRT-PCR that the expression of GmWRKY47 and GmWRKY 58 genes was decreased upon dehydration, and the expression of GmWRKY92, 144 and 165 genes was increased under salt treatment.

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Section: Resultsmentioning

confidence: 99%

Global Analysis of WRKY Genes and Their Response to Dehydration and Salt Stress in Soybean

et al. 2016

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“…Subgroup IIc has also been proposed to be a separate group by Zhang and Wang (2005) or subgroup Ib by Wu et al (2005). In addition to variations in zinc finger motifs, mutations in the consensus WRKYGQK sequence often appear in various plant species, and frequently observed variants include WRKYGKK and WRKYGEK (Wu et al 2005;Yao et al 2015;Jiang et al 2017b;Yang et al 2017;Song et al 2018).…”

Section: Wrky Structure and Evolutionmentioning

confidence: 99%

WRKY transcription factors: evolution, binding, and action

et al. 2019

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The WRKY transcription factor (TF) gene family expanded greatly in the evolutionary process from green algae to flowering plants through whole genome, segmental, and tandem duplications. Genomic sequences from diverse plant species provide valuable information about the origin and evolution of WRKY domain-containing proteins. Accumulating data indicate that WRKY TFs bind W-box and/or other cis-elements, revealing the specificity of ciselement recognition based on the structure of the WRKY protein as well as the nucleotides adjacent to the core sequences. Physical interactions among WRKY proteins or between WRKY proteins and other regulatory factors afford important insights into the regulation of this TF family. WRKY proteins are essential players in the kinase signaling network. The interaction of plant resistance (R) proteins with WRKY TFs and the existence of unusual chimeric R-WRKY proteins suggest diversity in signaling pathways for rapid immune responses. In this review, we focus mainly on progress in understanding the function of WRKY TFs in response to biotic stresses and focus on their multiple roles in Arabidopsis and rice plants.

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“…Thus, considering the vital role of WRKY TFs in various molecular, biological and physiological processes, the WRKY gene family has been extensively characterized in various crop plants (Zhang and Wang, 2005 ), such as rice (Ross et al, 2007 ), cucumber (Ling et al, 2011 ), maize (Wei et al, 2012 ), tomato (Huang et al, 2012 ), Castor bean (Li et al, 2012 ), physic nut (Xiong et al, 2013 ), barley (Liu et al, 2014 ), Brachypodium (Wen et al, 2014 ), Gossypium raimondii, G. hirsutum (Cai et al, 2014a ; Dou et al, 2014 ), grapevine (Wang et al, 2014 ), G. arboretum (Ding et al, 2015 ), cabbage (Yao et al, 2015 ), and in trees including rubber (Li et al, 2014 ), poplar (He et al, 2012 ; Jiang et al, 2014 ) and willow (Rao et al, 2015 ), and in Arabidopsis (de Pater et al, 1996 ; Deslandes et al, 2002 ; Song and Gao, 2014 ). However, no such studies have been reported in C 4 models, Setaria italica (foxtail millet) and S. viridis (green foxtail).…”

Section: Introductionmentioning

confidence: 99%

Global analysis of WRKY transcription factor superfamily in Setaria identifies potential candidates involved in abiotic stress signaling

et al. 2015

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Transcription factors (TFs) are major players in stress signaling and constitute an integral part of signaling networks. Among the major TFs, WRKY proteins play pivotal roles in regulation of transcriptional reprogramming associated with stress responses. In view of this, genome- and transcriptome-wide identification of WRKY TF family was performed in the C4model plants, Setaria italica (SiWRKY) and S. viridis (SvWRKY), respectively. The study identified 105 SiWRKY and 44 SvWRKY proteins that were computationally analyzed for their physicochemical properties. Sequence alignment and phylogenetic analysis classified these proteins into three major groups, namely I, II, and III with majority of WRKY proteins belonging to group II (53 SiWRKY and 23 SvWRKY), followed by group III (39 SiWRKY and 11 SvWRKY) and group I (10 SiWRKY and 6 SvWRKY). Group II proteins were further classified into 5 subgroups (IIa to IIe) based on their phylogeny. Domain analysis showed the presence of WRKY motif and zinc finger-like structures in these proteins along with additional domains in a few proteins. All SiWRKY genes were physically mapped on the S. italica genome and their duplication analysis revealed that 10 and 8 gene pairs underwent tandem and segmental duplications, respectively. Comparative mapping of SiWRKY and SvWRKY genes in related C4 panicoid genomes demonstrated the orthologous relationships between these genomes. In silico expression analysis of SiWRKY and SvWRKY genes showed their differential expression patterns in different tissues and stress conditions. Expression profiling of candidate SiWRKY genes in response to stress (dehydration and salinity) and hormone treatments (abscisic acid, salicylic acid, and methyl jasmonate) suggested the putative involvement of SiWRKY066 and SiWRKY082 in stress and hormone signaling. These genes could be potential candidates for further characterization to delineate their functional roles in abiotic stress signaling.

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Genome-wide identification and comparative expression analysis reveal a rapid expansion and functional divergence of duplicated genes in the WRKY gene family of cabbage, Brassica oleracea var. capitata

Cited by 38 publications

References 67 publications

Global Analysis of WRKY Genes and Their Response to Dehydration and Salt Stress in Soybean

Global Analysis of WRKY Genes and Their Response to Dehydration and Salt Stress in Soybean

WRKY transcription factors: evolution, binding, and action

Global analysis of WRKY transcription factor superfamily in Setaria identifies potential candidates involved in abiotic stress signaling

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