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
2022
Secondary Metabolism Gene Clusters Exhibit Increasingly Dynamic and Differential Expression during Asexual Growth, Conidiation, and Sexual Development in Neurospora crassa
Wang Z, Lopez-Giraldez F, Slot J, Yarden O, Trail F, Townsend JP. Secondary Metabolism Gene Clusters Exhibit Increasingly Dynamic and Differential Expression during Asexual Growth, Conidiation, and Sexual Development in Neurospora crassa. MSystems 2022, 7: e00232-22. PMID: 35638725, PMCID: PMC9239088, DOI: 10.1128/msystems.00232-22.Peer-Reviewed Original ResearchConceptsSM clustersComparative genomicsSecondary metabolitesAsexual growthN. crassaNeurospora crassaSecondary metabolism gene clustersSexual developmentDevelopmental stagesSecondary metabolite clustersComparative genomic analysisExtensive transcriptomic dataGene expression patternsEnvironmental conditionsFungal toxin productionLevel of RNASMC genesLife cycleRegulatory switchComputational annotationGene clusterEnvironmental signalsMetabolite clustersGenomic analysisKnockout phenotypes
2019
Integrative Activity of Mating Loci, Environmentally Responsive Genes, and Secondary Metabolism Pathways during Sexual Development of Chaetomium globosum
Wang Z, López-Giráldez F, Wang J, Trail F, Townsend JP. Integrative Activity of Mating Loci, Environmentally Responsive Genes, and Secondary Metabolism Pathways during Sexual Development of Chaetomium globosum. MBio 2019, 10: 10.1128/mbio.02119-19. PMID: 31822585, PMCID: PMC6904875, DOI: 10.1128/mbio.02119-19.Peer-Reviewed Original ResearchConceptsGene expressionMating lociFungal diversityResponsive genesSexual developmentSecondary metabolism gene clustersGenome-wide gene expressionMating-type genesRich fungal diversitySecondary metabolism pathwaysModel filamentous fungusSecondary metabolic pathwaysWide gene expressionNumerous secondary metabolitesGene expression responsesHistidine kinaseLife cycleSexual reproductionHomothallic speciesDevelopmental genesEvolutionary biologistsHeterokaryon incompatibilityAsexual reproductionDistinct morphological stagesEvolutionary historyComparative Genomics and Transcriptomics During Sexual Development Gives Insight Into the Life History of the Cosmopolitan Fungus Fusarium neocosmosporiellum
Kim W, Cavinder B, Proctor RH, O’Donnell K, Townsend JP, Trail F. Comparative Genomics and Transcriptomics During Sexual Development Gives Insight Into the Life History of the Cosmopolitan Fungus Fusarium neocosmosporiellum. Frontiers In Microbiology 2019, 10: 1247. PMID: 31231336, PMCID: PMC6568001, DOI: 10.3389/fmicb.2019.01247.Peer-Reviewed Original ResearchPolyketide synthase genesPerithecium developmentSynthase geneLife historySecondary metabolite gene clustersDiverse ecological nichesRoot rot pathogensComparative genomicsGene numberPlant pathogensLarger peritheciaGene clusterEcological nichesTransport genesMetabolic potentialGenomic underpinningsTranscriptomic analysisCosmopolitan fungusLarger ascosporesTransporter geneGenomeGenesNovel insightsField cropsSexual developmentMetabolism 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 switch
2018
Developmental Dynamics of Long Noncoding RNA Expression during Sexual Fruiting Body Formation in Fusarium graminearum
Kim W, Miguel-Rojas C, Wang J, Townsend JP, Trail F. Developmental Dynamics of Long Noncoding RNA Expression during Sexual Fruiting Body Formation in Fusarium graminearum. MBio 2018, 9: 10.1128/mbio.01292-18. PMID: 30108170, PMCID: PMC6094484, DOI: 10.1128/mbio.01292-18.Peer-Reviewed Original ResearchConceptsSmall RNA clustersSubset of lncRNAsRole of lncRNAsBody formationRNA clustersAntisense lncRNAsSexual developmentDevelopmental stage-specific expression patternsStage-specific expression patternsVegetative growthNonsense-mediated decay pathwayFundamental genomic resourcesMeiotic stagesHundreds of lncRNAsSense-antisense pairsGenome-wide analysisRNA surveillance systemLong Noncoding RNA ExpressionPlant pathogenic fungiNoncoding RNA ExpressionKey regulatory componentOpposite DNA strandsFruiting-body formationMajor staple cropDevelopmental transcriptome
2017
Light 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 developmentOpsin
2016
The 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 environment
2014
Gene Expression Differences among Three Neurospora Species Reveal Genes Required for Sexual Reproduction in Neurospora crassa
Lehr NA, Wang Z, Li N, Hewitt DA, López-Giráldez F, Trail F, Townsend JP. Gene Expression Differences among Three Neurospora Species Reveal Genes Required for Sexual Reproduction in Neurospora crassa. PLOS ONE 2014, 9: e110398. PMID: 25329823, PMCID: PMC4203796, DOI: 10.1371/journal.pone.0110398.Peer-Reviewed Original ResearchConceptsNeurospora crassaSexual reproductionN. crassaGenetic basisThree-dimensional fruiting bodiesSexual spore productionN. crassa geneBody developmentDiverse life historiesGenome-wide transcriptomicsSexual developmentStudy of meiosisGene expression differencesList of genesGene expression levelsMeiotic machineryMeiosis genesOrthologous genesSporulation genesNeurospora speciesGlomerella graminicolaEvolutionary timeAnimal taxaPerithecium formationLife history
2013
Global 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 specificity
2012
Transcriptome analyses during fruiting body formation in Fusarium graminearum and Fusarium verticillioides reflect species life history and ecology
Sikhakolli UR, López-Giráldez F, Li N, Common R, Townsend JP, Trail F. Transcriptome analyses during fruiting body formation in Fusarium graminearum and Fusarium verticillioides reflect species life history and ecology. Fungal Genetics And Biology 2012, 49: 663-673. PMID: 22705880, DOI: 10.1016/j.fgb.2012.05.009.Peer-Reviewed Original ResearchConceptsF. graminearumOrthologous genesLife historyFusarium graminearumF. verticillioidesGene expressionSexual developmentStage-specific gene expressionSpecies' life historyDifferent life historiesPrevious morphological analysesMorphological developmentLife cycleSexual sporesCereal pathogensUnclassified proteinsFunctional assignmentTranscriptional programsTranscriptome analysisTranscriptional analysisType genesEcological characteristicsApoptotic processFusarium speciesGraminearumDifferential impact of nutrition on developmental and metabolic gene expression during fruiting body development in Neurospora crassa
Wang Z, Lehr N, Trail F, Townsend JP. Differential impact of nutrition on developmental and metabolic gene expression during fruiting body development in Neurospora crassa. Fungal Genetics And Biology 2012, 49: 405-413. PMID: 22469835, PMCID: PMC3397380, DOI: 10.1016/j.fgb.2012.03.004.Peer-Reviewed Original ResearchConceptsCarrot agarPerithecial developmentNeurospora crassaNutritional resourcesCore metabolic genesDifferent fungiSexual developmentDiverse environmental stimuliMetabolic gene expressionKey regulatory roleDevelopmental programMetabolic genesMicroarray hybridizationTranscriptional profilesAnabolic pathwaysExpression patternsGene expressionBody sizeMetabolic differentiationRegulatory roleBody developmentEffects of nutritionNutritional environmentEnvironmental stimuliBody morphology
2010
Multi-targeted priming for genome-wide gene expression assays
Adomas AB, Lopez-Giraldez F, Clark TA, Wang Z, Townsend JP. Multi-targeted priming for genome-wide gene expression assays. BMC Genomics 2010, 11: 477. PMID: 20716356, PMCID: PMC3091673, DOI: 10.1186/1471-2164-11-477.Peer-Reviewed Original ResearchMeSH KeywordsDNA PrimersGene Expression ProfilingGene Expression Regulation, FungalGenes, FungalMetabolic Networks and PathwaysMyceliumNeurospora crassaNitrogenOligonucleotide Array Sequence AnalysisReproducibility of ResultsReverse Transcriptase Polymerase Chain ReactionReverse TranscriptionRNA, FungalRNA, MessengerSaccharomyces cerevisiaeSequence Analysis, RNAConceptsGene expressionGene expression assaysNeurospora crassaRibosomal RNAExpression assaysMost protein-coding genesEarly sexual developmentGenome-wide gene expressionTransfer RNA genesProtein-coding genesNitrogen starvation responseGenome of SaccharomycesPreponderance of genesGlobal gene expressionResponse of SaccharomycesCommon sequence motifsSexual developmentDetailed expression profilesReverse transcriptionRNA genesStarvation responseTag sequencingSequence motifsTransfer RNATranscriptomic assays