Genome-wide Identification and Structural, Functional and Evolutionary Analysis of WRKY Components of Mulberry

Baranwal, Vinay Kumar; Negi, Nisha; Khurana, Paramjit

doi:10.1038/srep30794

Cited by 43 publications

(31 citation statements)

References 59 publications

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“…Differential responses of several WRKYs are regulated by the presence of cis -elements in their promoter region [27,40,49]. For example, Morus 013217, which contains three LTREs in its promoter regions showed a strong response to cold stress [27]. Similar results were also found in our study.…”

Section: Discussionsupporting

confidence: 88%

Identification of WRKY Gene Family from Dimocarpus longan and Its Expression Analysis during Flower Induction and Abiotic Stress Responses

Jue

Sang

Liu

et al. 2018

IJMS

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Longan is an important fruit tree in the subtropical region of Southeast Asia and Australia. However, its blooming and its yield are susceptible to stresses such as droughts, high salinity, and high and low temperature. To date, the molecular mechanisms of abiotic stress tolerance and flower induction in longan have not been elucidated. WRKY transcription factors (TFs), which have been studied in various plant species, play important regulatory roles in plant growth, development, and responses to stresses. However, there is no report about WRKYs in longan. In this study, we identified 55 WRKY genes with the conserved WRKY domain and zinc finger motif in the longan genome. Based on the structural features of WRKY proteins and topology of the phylogenetic tree, the longan WRKY (DlWRKY) family was classified into three major groups (I–III) and five subgroups (IIa–IIe) in group II. Tissue expression analysis showed that 25 DlWRKYs were highly expressed in almost all organs, suggesting that these genes may be important for plant growth and organ development in longan. Comparative RNA-seq and qRT-PCR-based gene expression analysis revealed that 18 DlWRKY genes showed a specific expression during three stages of flower induction in “Sijimi” (“SJ”), which exhibited the “perpetual flowering” (PF) habit, indicating that these 18 DlWRKY genes may be involved in the flower induction and the genetic control of the perpetual flowering trait in longan. Furthermore, the RT-qPCR analysis illustrated the significant variation of 27, 18, 15, 17, 27, and 23 DlWRKY genes under SA (Salicylic acid), MeJA (Methyl Jasmonate), heat, cold, drought, or high salinity treatment, respectively, implicating that they might be stress- or hormone-responsive genes. In summary, we systematically and comprehensively analyzed the structure, evolution, and expression pattern of the DlWRKY genes. The results presented here increase our understanding of the WRKY family in fruit trees and provide a basis for the further elucidation of the biological function of DlWRKY genes in longan.

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Section: Discussionsupporting

confidence: 88%

Identification of WRKY Gene Family from Dimocarpus longan and Its Expression Analysis during Flower Induction and Abiotic Stress Responses

Jue

Sang

Liu

et al. 2018

IJMS

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“…PF00230 was then used to query the predicted Sugar beet proteome using HMMER 3.0 software ( http://hmmer.org/ ). 35 Arabidopsis AtAQPs were download from TAIR Database ( https://www.arabidopsis.org/browse/genefamily/Aquaporins.jsp ) and then used to search BvAQPs with BLASTp tool using NCBI sugar beet genome ( https://www.ncbi.nlm.nih.gov/genome/?term=Beta+vulgaris ) and sugar beet genome ( http://www.genomforschung.uni-bielefeld.de/en/projects/annobeet ) ( Baranwal, Negi & Khurana, 2016 ) with cut-off E -value of e −5 . All no-redundant gene sequences were analyzed by SMART ( http://smart.embl-heidelberg.de/ ) and Pfam ( http://pfam.xfam.org/search/sequence ).…”

Section: Methodsmentioning

confidence: 99%

Genome-wide identification and characterization of aquaporin gene family in Beta vulgaris

Kong

Yang

Wang

et al. 2017

PeerJ

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Aquaporins (AQPs) are essential channel proteins that execute multi-functions throughout plant growth and development, including water transport, uncharged solutes uptake, stress response, and so on. Here, we report the first genome-wide identification and characterization AQP (BvAQP) genes in sugar beet (Beta vulgaris), an important crop widely cultivated for feed, for sugar production and for bioethanol production. Twenty-eight sugar beet AQPs (BvAQPs) were identified and assigned into five subfamilies based on phylogenetic analyses: seven of plasma membrane (PIPs), eight of tonoplast (TIPs), nine of NOD26-like (NIPs), three of small basic (SIPs), and one of x-intrinsic proteins (XIPs). BvAQP genes unevenly mapped on all chromosomes, except on chromosome 4. Gene structure and motifs analyses revealed that BvAQP have conserved exon-intron organization and that they exhibit conserved motifs within each subfamily. Prediction of BvAQPs functions, based on key protein domains conservation, showed a remarkable difference in substrate specificity among the five subfamilies. Analyses of BvAQPs expression, by mean of RNA-seq, in different plant organs and in response to various abiotic stresses revealed that they were ubiquitously expressed and that their expression was induced by heat and salt stresses. These results provide a reference base to address further the function of sugar beet aquaporins and to explore future applications for plants growth and development improvements as well as in response to environmental stresses.

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“…Although, WRKY TFs are considered to be plant specific, however, their presence have been reported from unicellular algae, slime mold, and gymnosperms. The WRKY TFs have been reported from Arabidopsis , rice (74, 102 Baranwal et al, 2016 ), soybean (197, Schmutz et al, 2010 ), papaya, poplar, sorghum, Physcomitrella patens (66, 104, 68, 38, respectively, Pandey and Somssich, 2009 ) and Jatropha (58, Xiong et al, 2013 ). The WRKY family is acquires its name from the highly conserved 60 amino acid stretched WRKY domain, consisting of the highly conserved WRKYGQK at N-terminus and a novel metal chelating zinc finger signature at C-terminus.…”

Section: Introductionmentioning

confidence: 99%

Ectopic Expression of JcWRKY Transcription Factor Confers Salinity Tolerance via Salicylic Acid Signaling

et al. 2016

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Plants, being sessile, have developed intricate signaling network to specifically respond to the diverse environmental stress. The plant-specific WRKY TFs form one of the largest TF family and are involved in diverse plant processes, involving growth, development and stress signaling through auto and cross regulation with different genes and TFs. Here, we report the functional characterization of a salicylic acid -inducible JcWRKY TF. The JcWRKY overexpression confers salinity tolerance in transgenic tobacco, as was evident by increased chlorophyll content and seed germination potential. The transgenic plants showed increased soluble sugar, membrane stability, reduced electrolyte leakage and generation of reactive oxygen species (H2O2 and O2•-) as compared to the wild type. Furthermore, the low SA treatment along with salinity improved the tolerance potential of the transgenics by maintaining ROS homeostasis and high K+/Na+ ratio. The transcript expression of SA biosynthetic gene ICS1 and antioxidative enzymes (CAT and SOD) showed upregulation during stress. Thus, the present study reflects that JcWRKY is working in co-ordination with SA signaling to orchestrate the different biochemical and molecular pathways to maneuvre salt stress tolerance of the transgenic plants.

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Genome-wide Identification and Structural, Functional and Evolutionary Analysis of WRKY Components of Mulberry

Cited by 43 publications

References 59 publications

Identification of WRKY Gene Family from Dimocarpus longan and Its Expression Analysis during Flower Induction and Abiotic Stress Responses

Identification of WRKY Gene Family from Dimocarpus longan and Its Expression Analysis during Flower Induction and Abiotic Stress Responses

Genome-wide identification and characterization of aquaporin gene family in Beta vulgaris

Ectopic Expression of JcWRKY Transcription Factor Confers Salinity Tolerance via Salicylic Acid Signaling

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