Genome-wide identification of the potato WRKY transcription factor family

Zhang, Chao; Wang, Dongdong; Yang, Chan; Kong, Nana; Shi, Zheng Zheng; Zhao, Peng; Nan, Yunyou; Tengkun, Nie; Wang, Ruoqiu; Ma, Hongwei; Chen, Qin

doi:10.1371/journal.pone.0181573

Cited by 71 publications

(62 citation statements)

References 61 publications

(107 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Despite this, to date no studies have examined WRKY gene family components and their different characteristics in wild potato species. A few data on this gene family are available only in the cultivated potato, where Zhang et al 21 , Liu et al 22 and Cheng et al 12 identified 79, 82 and 81 StWRKYs, respectively. Previously, Dellagi et al 23 identified StWRKY1 as a good candidate for functional studies, and Shahzad et al 24 overexpressed it in potato.…”

mentioning

confidence: 99%

WRKY genes family study reveals tissue-specific and stress-responsive TFs in wild potato species

Villano

Esposito

D’Amelia

et al. 2020

Sci Rep

View full text Add to dashboard Cite

Wild potatoes, as dynamic resource adapted to various environmental conditions, represent a powerful and informative reservoir of genes useful for breeding efforts. WRKY transcription factors (TFs) are encoded by one of the largest families in plants and are involved in several biological processes such as growth and development, signal transduction, and plant defence against stress. In this study, 79 and 84 genes encoding putative WRKY TFs have been identified in two wild potato relatives, Solanum commersonii and S. chacoense. Phylogenetic analysis of WRKY proteins divided ScWRKYs and SchWRKYs into three Groups and seven subGroups. Structural and phylogenetic comparative analyses suggested an interspecific variability of WRKYs. Analysis of gene expression profiles in different tissues and under various stresses allowed to select ScWRKY045 as a good candidate in woundingresponse, ScWRKY055 as a bacterial infection triggered WRKY and ScWRKY023 as a multiple stressresponsive WRKY gene. Those WRKYs were further studied through interactome analysis allowing the identification of potential co-expression relationships between ScWRKYs/SchWRKYs and genes of various pathways. Overall, this study enabled the discrimination of WRKY genes that could be considered as potential candidates in both breeding programs and functional studies.Plants experience environmental constrains and pathogen attacks during their life. Being sessile organisms, their survival depends on the ability to properly and promptly reprogram cellular networks. Several and different classes of transcription factors (TFs) work as "master regulators" and "selector genes", being able to control processes that specify cell types and developmental patterning and modulate specific pathways. Among them, WRKY factors are drawing a great deal of interest in the scientific community due to their ability to simultaneously cope with multiple stresses 1,2 . They are notorious for coordinating signals in plant immunity response against several pathogens and pest attacks 3,4 . More recently, it has been confirmed that WRKYs also base defence mechanism to abiotic stresses and play a key role in cross-talk pathway networks between plant response and development 5,6 . Their involvement into multiple stress response and in plant growth regulation is evidenced by their W-box specific DNA binding 7,8 . Besides, WRKY binds sugar responsive elements and, very recently, it has been demonstrated that they activate sugar responsive genes through an epigenetic mechanism of control 9 . The systematic classification of components of the WRKY family is well organized. It is based on the WRKY binding domain (WD) characteristics along with those of the Zinc Finger (ZF) motif, which is typically present downstream the WD. WD consists of 60 amino acids structured as four-stranded β-sheets able to enter the major groove of B-form DNA. The highly conserved motif is "WRKYGQK". According to the number of WDs and the type of zinc finger motif, WRKY proteins can be classified into three Groups,...

show abstract

mentioning

confidence: 99%

WRKY genes family study reveals tissue-specific and stress-responsive TFs in wild potato species

Villano

Esposito

D’Amelia

et al. 2020

Sci Rep

View full text Add to dashboard Cite

show abstract

“…Correspondingly, it also had the shortest length of protein. Be different with other gene family, such as WRKY [28], the motifs in subgroup proteins had no significantly differences. Because the GH3 proteins combined amino acids to different acyl acid substrates, they must have had the corresponding active site.…”

Section: Structural Analysis Of Gh3 Proteinsmentioning

confidence: 66%

“…We defined paralogous genes as those existing in the same chromosome within a 50-kb physical distance that were tandem duplicated pairs [28,33]. The segmental duplication of each gene was ensured through Plant Genome Duplication Database (PGDD) website (http://chibba.agtec.uga.edu/duplication/).…”

Section: Analysis Of Gene Duplicationsmentioning

confidence: 99%

See 1 more Smart Citation

Evolutionary History of the GH3 Family Based on 48 Sequenced Plants and Identification of Jasmonic Acid-Relate GH3 Genes in <em>Solanum tuberosum</em>

Zhang¹,

Zhang²,

Wang³

et al. 2018

Preprint

Self Cite

View full text Add to dashboard Cite

Glycoside Hydrolase 3 (GH3) is a phytohormone-responsive family of genes that has been found in many plant species. It is implicated in the biological activity of indolacetic (IAA) and jasmonic acids (JA), and also affects plant growth and developmental processes and some stresses. In this study, GH3 genes were identified in 48 plants, which belong to algae, moss, fern, gymnosperm and angiosperm. No GH3 representative gene has been found in algae, and our research identified 4 genes in mosses, 19 in ferns, 7 in gymnosperms, and numerous in Angiosperms. The results showed that GH3 genes mainly occur in seed plants. Phylogenetic analysis of all GH3 genes showed three separate clades. Group I was related to JA adenylation, group II was related to IAA adenylation, and group III was separated from group II but the function was not clear. The structure of GH3 protein indicated highly conserved sequence in the plant kingdom. The analysis of JA-adenylation related to gene expression of GH3 in potato (Solanum tuberosum) showed that StGH3.12 highly responded to Methyl Jasmonate (MeJA) treatment. Expression levels of StGH3. 1, StGH3.11, and StGH3.12 were high in flower and StGH3.11 expression was also high in stolon. Our research revealed the evolution of the GH3 family, which is useful for studying the precise function about JA-adenylation GH3 genes in S. tuberosum under development and biotic stresses.

show abstract

“…We can obtain many genes that response to MYB transcription factor of F. tataricum under salt stress. As an important transcription factor superfamily, WRKY transporters are involved in response to environmental stimuli, such as high salt, low temperature, etc [52]. This transcription factor family in F. tataricum is highly up-regulate under salt stress, which has the complexity and importance of stress regulation.…”

Section: Discussionmentioning

confidence: 99%

Transcriptome analysis reveals salinity responses in four Tartary buckwheat cultivars

Song

Liu

Wang

et al. 2019

Preprint

View full text Add to dashboard Cite

12Tartary buckwheat (Fagopyrum tataricum) is an annual herbaceous crop with a higher content of rutin and 13 flavonoids than other crops. In order to understand the salt tolerance mechanism of Tartary buckwheat, we 14 conducted a transcriptome sequencing study. Two existing and two new salt-tolerant varieties of Tartary 15 buckwheat were used as experimental materials. These varieties were subjected to 100 mM NaCl for 48 16 hours treatment at the 3 leaf stage. Leaf RNA was extracted from 8 samples and performed RNA-seq. We de 17 novo assembled reads into a transcriptome dataset containing 62,637 unigenes with N50 length of 1596 bp. 18A total of 205. 2 million clean reads were obtained, and 33,495 (53.47%) of them were annotated. GO and 19 KEGG classification showed enrichment of these unigenes in 47 sub-categories, 25 KOG functional 20 categories and 129 pathways, respectively. With 11 contrasts, we obtained many differentially expressed 21 genes (DEGs) of transcriptome data in 8 samples. The relative expression of Unigene0009545 and 22Unigene0057231 in M1 and that of Unigene0023096 and Unigene0060321 in M2 was increased significantly 23 under salt stress and may be involved in salt tolerance. These findings will provide valuable reference 24 genetic information for the study on salt tolerance mechanism in plants and assist in cultivating strong 25 salt-tolerant varieties of Tartary buckwheat for greater yield in saline-alkali soil. 26

show abstract

Genome-wide identification of the potato WRKY transcription factor family

Cited by 71 publications

References 61 publications

WRKY genes family study reveals tissue-specific and stress-responsive TFs in wild potato species

WRKY genes family study reveals tissue-specific and stress-responsive TFs in wild potato species

Evolutionary History of the GH3 Family Based on 48 Sequenced Plants and Identification of Jasmonic Acid-Relate GH3 Genes in <em>Solanum tuberosum</em>

Transcriptome analysis reveals salinity responses in four Tartary buckwheat cultivars

Contact Info

Product

Resources

About