Featured Publications
The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomics
Wang Z, Kim W, Wang Y, Yakubovich E, Dong C, Trail F, Townsend J, Yarden O. The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomics. Frontiers In Fungal Biology 2023, 4: 1214537. PMID: 37746130, PMCID: PMC10512317, DOI: 10.3389/ffunb.2023.1214537.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsEvolutionary genomicsOmics dataFungal sexual developmentAncestral state analysisRichness of speciesDifferent taxonomic levelsAspects of biologySpecies/generaSystems biological analysisRegulatory network modelKnowledge of evolutionAscomycete genomesSordariomycetes classFungal evolutionTrait diversityDivergent lineagesFungal kingdomFungal biologyGenomic scaleSecondary metabolismModel genomesModel fungusModel speciesEcological diversityKey genetic elementsLight sensing by opsins and fungal ecology: NOP‐1 modulates entry into sexual reproduction in response to environmental cues
Wang Z, Wang J, Li N, Li J, Trail F, Dunlap JC, Townsend JP. Light sensing by opsins and fungal ecology: NOP‐1 modulates entry into sexual reproduction in response to environmental cues. Molecular Ecology 2017, 27: 216-232. PMID: 29134709, PMCID: PMC5797489, DOI: 10.1111/mec.14425.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceConserved SequenceEcological and Environmental PhenomenaFungal ProteinsGene Expression Regulation, FungalGene Knockout TechniquesGene Regulatory NetworksGenes, FungalLightModels, BiologicalMultienzyme ComplexesNADH, NADPH OxidoreductasesNeurospora crassaOpsinsOxidation-ReductionOxidative StressPhenotypePhylogenyProtein Structure, SecondaryReproductionUp-RegulationConceptsNOP-1Opsin-like proteinFungal ecologyPlant-associated fungiRapid environmental changeOxidative stress responseKey amino acidsFungal genomesComparative transcriptomicsSexual reproductionOrganismal functionNeurospora crassaEnvironmental cuesGenetic basisSensory rhodopsinStress responseNAD/NADPTransmembrane movementRetinal binding siteGenesAmino acidsFungiEnvironmental changesSexual developmentOpsinMetabolism and Development during Conidial Germination in Response to a Carbon-Nitrogen-Rich Synthetic or a Natural Source of Nutrition in Neurospora crassa
Wang Z, Miguel-Rojas C, Lopez-Giraldez F, Yarden O, Trail F, Townsend JP. Metabolism and Development during Conidial Germination in Response to a Carbon-Nitrogen-Rich Synthetic or a Natural Source of Nutrition in Neurospora crassa. MBio 2019, 10: 10.1128/mbio.00192-19. PMID: 30914504, PMCID: PMC6437048, DOI: 10.1128/mbio.00192-19.Peer-Reviewed Original ResearchConceptsDevelopmental regulatory genesVegetative growthAsexual reproductionConidial germinationRegulatory genesNutritional environmentLife historyNitrogen metabolismLife-history decisionsMode of reproductionAdaptive life historiesKnockout of genesGenome-wide transcriptomicsEarly life historySexual developmentMetabolic gene expressionReproductive dispersalSexual reproductionDevelopmental genesMetabolic genesNeurospora crassaDiverse ecosystemsNutrient conditionsGene expressionMajor switchA multigene phylogeny toward a new phylogenetic classification of Leotiomycetes
Johnston PR, Quijada L, Smith CA, Baral HO, Hosoya T, Baschien C, Pärtel K, Zhuang WY, Haelewaters D, Park D, Carl S, López-Giráldez F, Wang Z, Townsend JP. A multigene phylogeny toward a new phylogenetic classification of Leotiomycetes. IMA Fungus 2019, 10: 1. PMID: 32647610, PMCID: PMC7325659, DOI: 10.1186/s43008-019-0002-x.Peer-Reviewed Original ResearchGeneric type speciesType speciesITS gene treeEx-type specimensRibosomal DNA markersHigher taxonomic levelsNew phylogenetic classificationNature of taxaAero-aquatic hyphomycetesEnvironmental DNA extractsMulti-gene studiesDNA sequencing studiesIdentification of specimensGene treesFormal taxonomic changesMultigene phylogenyMammalian pathogensPlant pathogensNovel taxaAsexual morphNew genomesTaxonomic levelsClass LeotiomycetesDNA markersPhylogenetic classificationThe Fast-Evolving phy-2 Gene Modulates Sexual Development in Response to Light in the Model Fungus Neurospora crassa
Wang Z, Li N, Li J, Dunlap JC, Trail F, Townsend JP. The Fast-Evolving phy-2 Gene Modulates Sexual Development in Response to Light in the Model Fungus Neurospora crassa. MBio 2016, 7: 10.1128/mbio.02148-15. PMID: 26956589, PMCID: PMC4810495, DOI: 10.1128/mbio.02148-15.Peer-Reviewed Original ResearchConceptsModel fungus Neurospora crassaFungus Neurospora crassaSexual reproductionNeurospora crassaPHY-2Plant developmentPlant pathogensBacterial physiologyEnvironmental signalsSexual developmentSexual development-related genesEvolution of phytochromesDestructive plant pathogensDevelopment-related genesFungal growthRed light sensorFunction of phytochromeVariable light conditionsCritical roleFungal biologyPHY-1Asexual growthPhytochrome functionMost speciesPostfire environmentChapter One Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big Data
Dornburg A, Townsend JP, Wang Z. Chapter One Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big Data. Advances In Genetics 2017, 100: 1-47. PMID: 29153398, DOI: 10.1016/bs.adgen.2017.09.007.ChaptersConceptsTree of lifeFungal evolutionary biologyGenomic-scale dataHundreds of lociGenome-scale analysisFungal phylogenomicsFungal treeSpecies delimitationPhenotypic diversificationFirst genomeEvolutionary biologyPhylogenetic treePhylogenetic inferencePhylogenetic analysisEntire genomeTree inferenceReview of considerationsEvolutionary problemsPhylogenomicsGenomeTreesLociCentral roleExperimental designBiodiversitySex-specific gene expression during asexual development of Neurospora crassa
Wang Z, Kin K, López-Giráldez F, Johannesson H, Townsend JP. Sex-specific gene expression during asexual development of Neurospora crassa. Fungal Genetics And Biology 2012, 49: 533-543. PMID: 22626843, PMCID: PMC3397379, DOI: 10.1016/j.fgb.2012.05.004.Peer-Reviewed Original ResearchConceptsMating-type genesAsexual developmentMating typesNeurospora crassaGene expressionSex-specific gene expressionFungal life historyLight-responsive genesOverall gene expressionExpression levelsDifferent mating typesExpression of pheromonePheromone genesHigh expression levelsMat AType genesLife historyResponse genesExpression differencesDevelopment stagesGenesClonal developmentImpact of lightReceptor geneCrassaGlobal Gene Expression and Focused Knockout Analysis Reveals Genes Associated with Fungal Fruiting Body Development in Neurospora crassa
Wang Z, Lopez-Giraldez F, Lehr N, Farré M, Common R, Trail F, Townsend JP. Global Gene Expression and Focused Knockout Analysis Reveals Genes Associated with Fungal Fruiting Body Development in Neurospora crassa. MSphere 2013, 13: 154-169. PMID: 24243796, PMCID: PMC3910948, DOI: 10.1128/ec.00248-13.Peer-Reviewed Original ResearchConceptsPerithecial developmentNeurospora crassaGene expressionSexual developmentBody developmentFruiting-body developmentMost upregulated genesReverse genetics approachGlobal gene expressionSimilar expression patternsSame developmental stageMulticellular organismsSexual crossingMat AUnclassified proteinsDevelopmental traitsN. crassaKnockout analysisTranscriptomic landscapeType genesUpregulated genesGenetic basisDiverse functionsExpression patternsStage specificityToward a phylogenetic classification of the Leotiomycetes based on rDNA data
Wang Z, Johnston PR, Takamatsu S, Spatafora JW, Hibbett DS. Toward a phylogenetic classification of the Leotiomycetes based on rDNA data. Mycologia 2006, 98: 1065-1075. PMID: 17486981, DOI: 10.3852/mycologia.98.6.1065.Peer-Reviewed Original ResearchContributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi).
Matheny PB, Wang Z, Binder M, Curtis JM, Lim YW, Nilsson RH, Hughes KW, Hofstetter V, Ammirati JF, Schoch CL, Langer E, Langer G, McLaughlin DJ, Wilson AW, Frøslev T, Ge ZW, Kerrigan RW, Slot JC, Yang ZL, Baroni TJ, Fischer M, Hosaka K, Matsuura K, Seidl MT, Vauras J, Hibbett DS. Contributions of rpb2 and tef1 to the phylogeny of mushrooms and allies (Basidiomycota, Fungi). Molecular Phylogenetics And Evolution 2007, 43: 430-51. PMID: 17081773, DOI: 10.1016/j.ympev.2006.08.024.Peer-Reviewed Original ResearchA higher-level phylogenetic classification of the Fungi.
Hibbett DS, Binder M, Bischoff JF, Blackwell M, Cannon PF, Eriksson OE, Huhndorf S, James T, Kirk PM, Lücking R, Thorsten Lumbsch H, Lutzoni F, Matheny PB, McLaughlin DJ, Powell MJ, Redhead S, Schoch CL, Spatafora JW, Stalpers JA, Vilgalys R, Aime MC, Aptroot A, Bauer R, Begerow D, Benny GL, Castlebury LA, Crous PW, Dai YC, Gams W, Geiser DM, Griffith GW, Gueidan C, Hawksworth DL, Hestmark G, Hosaka K, Humber RA, Hyde KD, Ironside JE, Kõljalg U, Kurtzman CP, Larsson KH, Lichtwardt R, Longcore J, Miadlikowska J, Miller A, Moncalvo JM, Mozley-Standridge S, Oberwinkler F, Parmasto E, Reeb V, Rogers JD, Roux C, Ryvarden L, Sampaio JP, Schüssler A, Sugiyama J, Thorn RG, Tibell L, Untereiner WA, Walker C, Wang Z, Weir A, Weiss M, White MM, Winka K, Yao YJ, Zhang N. A higher-level phylogenetic classification of the Fungi. Mycological Research 2007, 111: 509-47. PMID: 17572334, DOI: 10.1016/j.mycres.2007.03.004.Peer-Reviewed Original ResearchEvolution of Reproductive Morphology in Leaf Endophytes
Wang Z, Johnston PR, Yang ZL, Townsend JP. Evolution of Reproductive Morphology in Leaf Endophytes. PLOS ONE 2009, 4: e4246. PMID: 19158947, PMCID: PMC2617777, DOI: 10.1371/journal.pone.0004246.Peer-Reviewed Original ResearchConceptsLeaf endophytesEcological roleDead host tissuesCommon developmental pathwayEndophytic lifestyleAsexual developmentSaprobic speciesReproductive structuresReproductive morphologySaprobic fungiFungal tissueFungal classificationDead woodEndophytic fungiDevelopmental pathwaysBody sizeFungal morphologySignificant divergenceLeotiomycetesFungiEndophytesHost tissuesProblematic groupRhytismatalesImportant roleLife history and systematics of the aquatic discomycete Mitrula (Helotiales, Ascomycota) based on cultural, morphological, and molecular studies
Wang Z, Binder M, Hibbett DS. Life history and systematics of the aquatic discomycete Mitrula (Helotiales, Ascomycota) based on cultural, morphological, and molecular studies. American Journal Of Botany 2005, 92: 1565-1574. PMID: 21646174, DOI: 10.3732/ajb.92.9.1565.Peer-Reviewed Original ResearchM. elegansParsimony analysisLife historySmall subunit rDNAUnknown life historySequences of rDNAPhylogenetic relationshipsSubunit rDNASubunit DNAElegansHerbarium materialMolecular techniquesLikelihood analysisMolecular studiesHelotialesCladeRDNASpeciesPure coloniesConidiaNorth AmericaBayesian analysisHelotiaceaeSclerotiniaceaeUncertain positionEvolution of helotialean fungi (Leotiomycetes, Pezizomycotina): A nuclear rDNA phylogeny
Wang Z, Binder M, Schoch CL, Johnston PR, Spatafora JW, Hibbett DS. Evolution of helotialean fungi (Leotiomycetes, Pezizomycotina): A nuclear rDNA phylogeny. Molecular Phylogenetics And Evolution 2006, 41: 295-312. PMID: 16837216, DOI: 10.1016/j.ympev.2006.05.031.Peer-Reviewed Original ResearchConceptsHelotialean fungiMolecular phylogenyBasal lineagePhylogenetic distributionRDNA phylogenyWider taxonLSU rDNARDNA regionMultiple cladesEcological factorsHelotialesLeotiomycetesPhylogenyRDNACladeProblematic groupFungiTraditional classificationBayesian analysisDivergent characterCurrent classificationMyxotrichaceaeEndophytismDeep relationshipGeoglossomycetesToward a phylogenetic classification of the Leotiomycetes based on rDNA data
Wang Z, Johnston P, Takamatsu S, Spatafora J, Hibbett D. Toward a phylogenetic classification of the Leotiomycetes based on rDNA data. Mycologia 2006, 98: 1065-1075. DOI: 10.1080/15572536.2006.11832634.Peer-Reviewed Original ResearchA new species of Cudonia based on morphological and molecular data
Wang Z, Binder M, Hibbett D. A new species of Cudonia based on morphological and molecular data. Mycologia 2002, 94: 641-650. PMID: 21156537, DOI: 10.1080/15572536.2003.11833192.Peer-Reviewed Original Research
2024
Assessing vaginal microbiome through Vaginal Microecology Evaluation System as a predictor for in vitro fertilization outcomes: a retrospective study
Tian Q, Jin S, Zhang G, Liu Y, Liu J, Tang X, Li Y, Liu J, Liu Y, Wang Z. Assessing vaginal microbiome through Vaginal Microecology Evaluation System as a predictor for in vitro fertilization outcomes: a retrospective study. Frontiers In Endocrinology 2024, 15: 1380187. PMID: 39045277, PMCID: PMC11263289, DOI: 10.3389/fendo.2024.1380187.Peer-Reviewed Original ResearchControlled ovarian stimulationLive birth rateIVF-ETIVF-ET treatmentVaginal microbiomeBacterial vaginosisPregnancy outcomesEmbryo transferRetrospective analysis of pregnancy outcomesSuccess rate of IVF-ETIn vitro fertilization outcomesAnalysis of pregnancy outcomesFresh embryo transferIVF-ET outcomeEarly miscarriage rateIVF-ET proceduresProportion of patientsMultivariate logistic regression modelBirth rateProcess of in vitro fertilizationMiscarriage rateOvarian stimulationTubal factorPatient ageVaginal microenvironmentSeparation and purification of benzylester glucosides and derivatives from tubers of Gymnadenia conopsea (L.) R. Br. by linear gradient counter‐current chromatography combined with elution‐extrusion mode
Feng Q, Zhang Z, Sun M, Wang Z, Xu X, Chen Q, Cheng Y, Yin Z, Dong H, Feng Y, Wang D. Separation and purification of benzylester glucosides and derivatives from tubers of Gymnadenia conopsea (L.) R. Br. by linear gradient counter‐current chromatography combined with elution‐extrusion mode. Journal Of Separation Science 2024, 47: e2400118. PMID: 39031866, DOI: 10.1002/jssc.202400118.Peer-Reviewed Original ResearchConceptsElution-extrusion modeCounter-current chromatographyComplex natural productsNuclear magnetic resonance spectrometryHighly polar compoundsMagnetic resonance spectrometryDactylorhin BTubers of Gymnadenia conopseaMobile phaseMass spectrometryBenzylesterHigh polarizationSample loadingGymnadenia conopseaSeparation parametersNatural productsDerivativesDactylorhin ASpectrometryRatio of mobile phaseEffective active componentsCompoundsFood homology plantLoroglossinSeparationMeta‐analysis reveals that rheumatoid arthritis is associated with worse clinical outcomes among patients with COVID‐19
Zhang G, Liu J, Wang J, Wang Z, Zhang J, Ding Y, Tang X, Wang W, Liu J, Liu Y, Liu J, Xu X. Meta‐analysis reveals that rheumatoid arthritis is associated with worse clinical outcomes among patients with COVID‐19. International Journal Of Rheumatic Diseases 2024, 27 DOI: 10.1111/1756-185x.15049.Peer-Reviewed Original ResearchRA patientsClinical outcomesRheumatoid arthritisMeta-analysisAssociated with worse clinical outcomesIncreased risk of adverse clinical outcomesRisk of adverse clinical outcomesAdverse clinical outcomesNon-RA patientsRisk of publication biasSystematic literature searchNo significant differenceCOVID-19 infectionMechanical ventilationClinical severityAdverse outcomesICU admissionIncreased riskVulnerable to coronavirus diseaseEgger's testPatientsElectronic databasesRatings of severityPublication biasCoronavirus disease 2019
2023
Lineage-specific genes are clustered with HET-domain genes and respond to environmental and genetic manipulations regulating reproduction in Neurospora
Wang Z, Wang Y, Kasuga T, Lopez-Giraldez F, Zhang Y, Zhang Z, Wang Y, Dong C, Sil A, Trail F, Yarden O, Townsend J. Lineage-specific genes are clustered with HET-domain genes and respond to environmental and genetic manipulations regulating reproduction in Neurospora. PLOS Genetics 2023, 19: e1011019. PMID: 37934795, PMCID: PMC10684091, DOI: 10.1371/journal.pgen.1011019.Peer-Reviewed Original ResearchConceptsLineage-specific genesHET domain genesSexual reproductionFunctional roleUnusual carbon sourcesPotential functional roleMating lociAsexual growthGenetic mutantsNeurospora crassaPossible functional roleSexual phaseGenetic manipulationTranscriptomic profilingReproduction regulationGene knockoutPP-1ADV-1Environmental alterationsGenesSexual developmentNeurosporaReproductionCarbon sourceGenetic barrier