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Genome-wide identification and characterization of cacao WRKY transcription factors and analysis of their expression in response to witches' broom disease

https://doi.org/10.1371/journal.pone.0187346

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Product Differentiation by Analysis of DNA Melting Curves during the Polymerase Chain Reaction

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Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure

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Characterization of a cDNA encoding a novel DNA-binding protein, SPF1, that recognizes SP8 sequences in the 5′ upstream regions of genes coding for sporamin and β-amylase from sweet potato

inferredcites →https://doi.org/10.1007/s00122-004-1662-4openalex-snapshot

Isolation, characterization, and development of WRKY genes as useful genetic markers in Theobroma cacao

inferredcites →https://doi.org/10.1007/s00299-013-1469-3openalex-snapshot

Overexpression of AtWRKY28 and AtWRKY75 in Arabidopsis enhances resistance to oxalic acid and Sclerotinia sclerotiorum

inferredcites →https://doi.org/10.1007/s00425-004-1253-2openalex-snapshot

Characterization of a WRKY transcription factor expressed in late torpedo-stage embryos of Solanum chacoense

inferredcites →https://doi.org/10.1007/s00438-012-0696-6openalex-snapshot

Genome-wide analysis of WRKY transcription factors in Solanum lycopersicum

inferredcites →https://doi.org/10.1007/s10709-011-9599-4openalex-snapshot

WRKY gene family evolution in Arabidopsis thaliana

inferredcites →https://doi.org/10.1007/s11103-004-2142-6openalex-snapshot

Targets of the WRKY53 transcription factor and its role during leaf senescence in Arabidopsis

inferredcites →https://doi.org/10.1007/s11103-013-0032-5openalex-snapshot

OsWRKY28, a PAMP-responsive transrepressor, negatively regulates innate immune responses in rice against rice blast fungus

inferredcites →https://doi.org/10.1016/j.chom.2008.02.010openalex-snapshot

Plant NB-LRR Immune Receptors: From Recognition to Transcriptional Reprogramming

inferredcites →https://doi.org/10.1016/j.cj.2014.03.001openalex-snapshot

Genome-wide analysis of the WRKY transcription factor gene family in Gossypium raimondii and the expression of orthologs in cultivated tetraploid cotton

inferredcites →https://doi.org/10.1016/j.plantsci.2007.04.006openalex-snapshot

Involvement of calcium oxalate degradation during programmed cell death in Theobroma cacao tissues triggered by the hemibiotrophic fungus Moniliophthora perniciosa

inferredcites →https://doi.org/10.1016/j.plaphy.2011.05.004openalex-snapshot

Hydrogen peroxide formation in cacao tissues infected by the hemibiotrophic fungus Moniliophthora perniciosa

inferredcites →https://doi.org/10.1016/j.tplants.2010.02.006openalex-snapshot

WRKY transcription factors

inferredcites →https://doi.org/10.1016/j.ympev.2007.06.012openalex-snapshot

The potential of the WRKY gene family for phylogenetic reconstruction: An example from the Malvaceae

inferredcites →https://doi.org/10.1016/s0959-440x(02)00314-7openalex-snapshot

Transcription factor complexes

inferredcites →https://doi.org/10.1016/s1360-1385(00)01600-9openalex-snapshot

The WRKY superfamily of plant transcription factors

inferredcites →https://doi.org/10.1038/ng.736openalex-snapshot

The genome of Theobroma cacao

inferredcites →https://doi.org/10.1038/nrg3901openalex-snapshot

Genetic mechanisms of abiotic stress tolerance that translate to crop yield stability

inferredcites →https://doi.org/10.1039/c2mb05421copenalex-snapshot

Transcriptomics and systems biology analysis in identification of specific pathways involved in cacao resistance and susceptibility to witches' broom disease

inferredcites →https://doi.org/10.1046/j.1365-3059.2003.00865.xopenalex-snapshot

An optimized screening method for identifying levels of resistance to Crinipellis perniciosa in cocoa ( Theobroma cacao )

inferredcites →https://doi.org/10.1080/0028825x.2003.9512860openalex-snapshot

Witches’ brooms and frosty pods: Two major pathogens of cacao

inferredcites →https://doi.org/10.1089/cmb.2005.12.1047openalex-snapshot

Comprehensive Algorithm for Quantitative Real-Time Polymerase Chain Reaction

inferredcites →https://doi.org/10.1093/aob/mcm092openalex-snapshot

Comparative Analysis of Expressed Genes from Cacao Meristems Infected by Moniliophthora perniciosa

inferredcites →https://doi.org/10.1093/bioinformatics/14.1.48openalex-snapshot

Combining evidence using p-values: application to sequence homology searches.

inferredcites →https://doi.org/10.1093/bioinformatics/14.9.817openalex-snapshot

MODELTEST: testing the model of DNA substitution.

inferredcites →https://doi.org/10.1093/jxb/ern045openalex-snapshot

Structure–function analysis of the NB-ARC domain of plant disease resistance proteins

inferredcites →https://doi.org/10.1093/jxb/err450openalex-snapshot

WRKY54 and WRKY70 co-operate as negative regulators of leaf senescence in Arabidopsis thaliana

inferredcites →https://doi.org/10.1093/jxb/eru381openalex-snapshot

Genome-wide identification and characterization of the Populus WRKY transcription factor family and analysis of their expression in response to biotic and abiotic stresses

inferredcites →https://doi.org/10.1093/jxb/erv125openalex-snapshot

CaWRKY6 transcriptionally activates CaWRKY40, regulates Ralstonia solanacearum resistance, and confers high-temperature and high-humidity tolerance in pepper

inferredcites →https://doi.org/10.1093/jxb/erv334openalex-snapshot

TwoTheobroma cacaogenotypes with contrasting pathogen tolerance show aberrant transcriptional and ROS responses after salicylic acid treatment

inferredcites →https://doi.org/10.1093/molbev/msr121openalex-snapshot

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

inferredcites →https://doi.org/10.1093/nar/gkh340openalex-snapshot

MUSCLE: multiple sequence alignment with high accuracy and high throughput

inferredcites →https://doi.org/10.1093/nar/gkp335openalex-snapshot

MEME SUITE: tools for motif discovery and searching

inferredcites →https://doi.org/10.1093/nar/gkr1293openalex-snapshot

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a040454openalex-snapshot

The neighbor-joining method: a new method for reconstructing phylogenetic trees.

inferredcites →https://doi.org/10.1093/treephys/tpv084openalex-snapshot

Isolation and characterization of a subgroup IIa WRKY transcription factor PtrWRKY40 fromPopulus trichocarpa

inferredcites →https://doi.org/10.1094/mpmi-23-5-0558openalex-snapshot

Wounding-Induced WRKY8 Is Involved in Basal Defense in Arabidopsis

inferredcites →https://doi.org/10.1104/pp.103.034967openalex-snapshot

A Rice WRKY Gene Encodes a Transcriptional Repressor of the Gibberellin Signaling Pathway in Aleurone Cells

inferredcites →https://doi.org/10.1104/pp.111.181834openalex-snapshot

The Transcription Factor CrWRKY1 Positively Regulates the Terpenoid Indole Alkaloid Biosynthesis in Catharanthus roseus

inferredcites →https://doi.org/10.1105/tpc.001404openalex-snapshot

TRANSPARENT TESTA GLABRA2 , a Trichome and Seed Coat Development Gene of Arabidopsis, Encodes a WRKY Transcription Factor

inferredcites →https://doi.org/10.1105/tpc.105.037523openalex-snapshot

Physical and Functional Interactions between Pathogen-Induced Arabidopsis WRKY18, WRKY40, and WRKY60 Transcription Factors

inferredcites →https://doi.org/10.1111/j.1364-3703.2011.00731.xopenalex-snapshot

Building a mutant resource for the study of disease resistance in rice reveals the pivotal role of several genes involved in defence

inferredcites →https://doi.org/10.1111/j.1365-313x.2008.03651.xopenalex-snapshot

The Arabidopsis transcription factor WRKY27 influences wilt disease symptom development caused by Ralstonia solanacearum

inferredcites →https://doi.org/10.1111/j.1365-313x.2010.04232.xopenalex-snapshot

WRKY72‐type transcription factors contribute to basal immunity in tomato and Arabidopsis as well as gene‐for‐gene resistance mediated by the tomato R gene Mi‐1

inferredcites →https://doi.org/10.1111/j.1365-313x.2010.04387.xopenalex-snapshot

Transcriptional reprogramming regulated by WRKY18 and WRKY40 facilitates powdery mildew infection of Arabidopsis

inferredcites →https://doi.org/10.1111/j.1744-7909.2007.00504.xopenalex-snapshot

The WRKY Gene Family in Rice ( Oryza sativa )

inferredcites →https://doi.org/10.1111/nph.12378openalex-snapshot

Defense‐related transcription factors WRKY 70 and WRKY 54 modulate osmotic stress tolerance by regulating stomatal aperture in A rabidopsis

inferredcites →https://doi.org/10.1111/ppa.12224openalex-snapshot

The infection process of M oniliophthora perniciosa in cacao

inferredcites →https://doi.org/10.1111/tpj.12051openalex-snapshot

A t MYB 44 regulates WRKY 70 expression and modulates antagonistic interaction between salicylic acid and jasmonic acid signaling

inferredcites →https://doi.org/10.1146/annurev.phyto.34.1.573openalex-snapshot

STATUS OF CACAO WITCHES' BROOM: Biology, Epidemiology, and Management

inferredcites →https://doi.org/10.1155/2014/434072openalex-snapshot

Evaluation and Integration of Genetic Signature for Prediction Risk of Nasopharyngeal Carcinoma in Southern China

inferredcites →https://doi.org/10.1155/2014/787680openalex-snapshot

Identification and Characterization of the Grape WRKY Family

inferredcites →https://doi.org/10.1186/1471-2148-5-1openalex-snapshot

The WRKY transcription factor superfamily: its origin in eukaryotes and expansion in plants

inferredcites →https://doi.org/10.1186/1471-2164-16-1openalex-snapshot

Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing

inferredcites →https://doi.org/10.1186/1471-2164-9-194openalex-snapshot

Phylogenetic and comparative gene expression analysis of barley (Hordeum vulgare) WRKY transcription factor family reveals putatively retained functions between monocots and dicots

inferredcites →https://doi.org/10.1186/1471-2164-9-s2-s6openalex-snapshot

In silico comparison of transcript abundances during Arabidopsis thaliana and Glycine max resistance to Fusarium virguliforme

inferredcites →https://doi.org/10.1186/1471-2229-14-1openalex-snapshot

Glycoprotein composition along the pistil of Malus x domestica and the modulation of pollen tube growth

inferredcites →https://doi.org/10.1186/1471-2229-14-161openalex-snapshot

The pathogenesis-related protein PR-4b from Theobroma cacao presents RNase activity, Ca2+ and Mg2+ dependent-DNase activity and antifungal action on Moniliophthora perniciosa

inferredcites →https://doi.org/10.1186/s12864-015-1346-2openalex-snapshot

RNASeqBrowser: A genome browser for simultaneous visualization of raw strand specific RNAseq reads and UCSC genome browser custom tracks

inferredcites →https://doi.org/10.1186/s12864-015-2057-4openalex-snapshot

The WRKY transcription factor family and senescence in switchgrass

inferredcites →https://doi.org/10.1371/journal.pgen.1004384openalex-snapshot

Phosphorylation of a WRKY Transcription Factor by MAPKs Is Required for Pollen Development and Function in Arabidopsis

inferredcites →https://doi.org/10.1371/journal.pone.0113092openalex-snapshot

Genome-Wide Investigation and Expression Profiling of AP2/ERF Transcription Factor Superfamily in Foxtail Millet (Setaria italica L.)

inferredcites →https://doi.org/10.1590/s1984-70332011000500011openalex-snapshot

Cacao breeding in Bahia, Brazil: strategies and results

inferredcites →https://doi.org/10.21757/0103-3816.2012v24n1p27-30openalex-snapshot

ASSOCIATION AMONG SOURCES OF RESISTANCE TO WITCHES' BROOM DISEASE FOR THE INCREMENT OF THE LEVEL AND DURABILITY OF THE CHARACTER

inferredcites →https://doi.org/10.3389/fpls.2015.00001openalex-snapshot

Control of yellow and purple nutsedge in elevated CO2 environments with glyphosate and halosulfuron

inferredcites →https://doi.org/10.3389/fpls.2015.00563openalex-snapshot

Application of genomics-assisted breeding for generation of climate resilient crops: progress and prospects

inferredcites →https://doi.org/10.3852/mycologia.97.5.1012openalex-snapshot

The causal agents of witches' broom and frosty pod rot of cacao (chocolate, Theobroma cacao) form a new lineage of Marasmiaceae

inferredcites →https://doi.org/10.4238/2011.november.17.4openalex-snapshot

Establishing references for gene expression analyses by RT-qPCR in Theobroma cacao tissues

inferredcites →https://doi.org/10.4238/vol9-3gmr825openalex-snapshot

Expression analysis of transcription factors from the interaction between cacao and Moniliophthora perniciosa (Tricholomataceae)

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.2139/ssrn.4752319openalex-extracted

Selection in Common Cocoa Half-Sibling Progenies for Resistance to Witches’ Broom in Brazilian Cultivation

inferred← citeshttps://doi.org/10.1007/978-3-031-09293-0_2openalex-snapshot

Genomic Designing for Biotic Stress Resistant Cocoa Tree

inferred← citeshttps://doi.org/10.1007/978-981-15-9380-2_11openalex-snapshot

Role of WRKY Transcription Factor Superfamily in Plant Disease Management

inferred← citeshttps://doi.org/10.1007/s00468-019-01860-3openalex-snapshot

Transcriptome-wide identification of WRKY family genes and their expression under cold acclimation in Eucalyptus globulus

inferred← citeshttps://doi.org/10.1007/s10709-025-00227-6openalex-snapshot

Comparative analysis of the WRKY gene family between Chimonanthus praecox and C. salicifolius

inferred← citeshttps://doi.org/10.1007/s11295-021-01490-2openalex-snapshot

Selection and validation of reference genes for accurate RT-qPCR gene expression normalization in cacao beans during fermentation

inferred← citeshttps://doi.org/10.1007/s13258-018-00780-9openalex-snapshot

Genome-wide identification and expression analyses of WRKY transcription factor family members from chickpea (Cicer arietinum L.) reveal their role in abiotic stress-responses

inferred← citeshttps://doi.org/10.1007/s13258-018-0734-9openalex-snapshot

Genome-wide identification of WRKY family genes and their response to abiotic stresses in tea plant (Camellia sinensis)

inferred← citeshttps://doi.org/10.1007/s13258-021-01118-8openalex-snapshot

Transcriptome-wide characterization of the WRKY family genes in Lonicera macranthoides and the role of LmWRKY16 in plant senescence

inferred← citeshttps://doi.org/10.1016/j.ijbiomac.2023.124379openalex-snapshot

Progress in the understanding of WRKY transcription factors in woody plants

inferred← citeshttps://doi.org/10.1080/17429145.2022.2144650openalex-snapshot

Comparative transcriptomics of cupuassu ( Theobroma grandiflorum ) offers insights into the early defense mechanism to Moniliophthora perniciosa , the causal agent of witches’ broom disease

inferred← citeshttps://doi.org/10.1094/phyto-10-20-0480-ropenalex-snapshot

WRKY Transcription Factors Actively Respond to Fusarium oxysporum in Lilium regale

inferred← citeshttps://doi.org/10.1101/2021.01.27.425041openalex-snapshot

The GASA Gene Family in Theobroma cacao : Genome wide Identification and Expression Analysis

inferred← citeshttps://doi.org/10.11144/javeriana.10554.60740openalex-snapshot

Análisis fisiológico y transcriptómico de la respuesta a déficit hídrico en cacao (Theobroma cacao L.) para la identificación de genes candidatos de tolerancia a estrés

inferred← citeshttps://doi.org/10.1134/s1021443724604166openalex-snapshot

Putative Molecular Aspects of Succinic Semialdehyde Dehydrogenase’s Operation in the Leaves of Wheat (Triticum aestivum L.) under Salt Stress

inferred← citeshttps://doi.org/10.1186/s12870-022-03511-1openalex-snapshot

Characterization of the WRKY gene family in Akebia trifoliata and their response to Colletotrichum acutatum

inferred← citeshttps://doi.org/10.1186/s12870-026-09047-yopenalex-snapshot

Pan-genomic and pan-transcriptomic integration unveils evolutionary dynamics and regulatory diversification of the WRKY gene family in Camellia sinensis

inferred← citeshttps://doi.org/10.31857/s0015330324010088openalex-snapshot

Предполагаемые молекулярные аспекты функционирования дегидрогеназы полуальдегида янтарной кислоты в листьях пшеницы (Triticum aestivum L.) при солевом стрессе

inferred← citeshttps://doi.org/10.3389/fevo.2021.707708openalex-snapshot

The BAHD Gene Family in Cacao (Theobroma cacao, Malvaceae): Genome-Wide Identification and Expression Analysis

inferred← citeshttps://doi.org/10.3389/fgene.2023.1172321openalex-snapshot

Genome-wide identification and bioinformatics analysis of the WRKY transcription factors and screening of candidate genes for anthocyanin biosynthesis in azalea (Rhododendron simsii)

inferred← citeshttps://doi.org/10.3389/fpls.2021.780805openalex-snapshot

Changes in Gene Expression in Leaves of Cacao Genotypes Resistant and Susceptible to Phytophthora palmivora Infection

inferred← citeshttps://doi.org/10.3389/fpls.2023.1238507openalex-snapshot

Plant salinity stress, sensing, and its mitigation through WRKY

inferred← citeshttps://doi.org/10.3390/agronomy10111634openalex-snapshot

Genome-Wide Identification and Analysis of the WRKY Gene Family in the Xerophytic Evergreen Ammopiptanthus nanus

inferred← citeshttps://doi.org/10.3390/agronomy11071425openalex-snapshot

The GASA Gene Family in Cacao (Theobroma cacao, Malvaceae): Genome Wide Identification and Expression Analysis

inferred← citeshttps://doi.org/10.3390/agronomy11081651openalex-snapshot

Magnesium transporter Gene Family: Genome-Wide Identification and Characterization in Theobroma cacao, Corchorus capsularis, and Gossypium hirsutum of Family Malvaceae

inferred← citeshttps://doi.org/10.3390/genes10050360openalex-snapshot

Genome-Wide Identification of WRKY Transcription Factors in Chinese jujube (Ziziphus jujuba Mill.) and Their Involvement in Fruit Developing, Ripening, and Abiotic Stress

inferred← citeshttps://doi.org/10.3390/genes12111799openalex-snapshot

Genome-Wide Identification and Analysis of the MADS-Box Gene Family in Theobroma cacao

inferred← citeshttps://doi.org/10.3390/genes13061068openalex-snapshot

Genome-Wide Analysis of the WRKY Gene Family in Malus domestica and the Role of MdWRKY70L in Response to Drought and Salt Stresses

inferred← citeshttps://doi.org/10.3390/genes13091572openalex-snapshot

Genome-Wide Identification and Analysis of the R2R3-MYB Gene Family in Theobroma cacao

inferred← citeshttps://doi.org/10.3390/genes14010057openalex-snapshot

Genome-Wide Identification and Analysis of the GRAS Transcription Factor Gene Family in Theobroma cacao

inferred← citeshttps://doi.org/10.3390/ijms232315396openalex-snapshot

Genome and Transcriptome-Wide Analysis of OsWRKY and OsNAC Gene Families in Oryza sativa and Their Response to White-Backed Planthopper Infestation

inferred← citeshttps://doi.org/10.3390/plants8100393openalex-snapshot

Genome-Wide Identification of WRKY Transcription Factors in the Asteranae

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