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 ResearchMeSH KeywordsFungal ProteinsGene Expression ProfilingGenes, FungalNeurosporaNeurospora crassaPhenotypeReproductionConceptsLineage-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 barrierComparative Transcriptomics of Fusarium graminearum and Magnaporthe oryzae Spore Germination Leading up To Infection
Miguel-Rojas C, Cavinder B, Townsend J, Trail F. Comparative Transcriptomics of Fusarium graminearum and Magnaporthe oryzae Spore Germination Leading up To Infection. MBio 2023, 14: e02442-22. PMID: 36598191, PMCID: PMC9973345, DOI: 10.1128/mbio.02442-22.Peer-Reviewed Original ResearchConceptsComparative transcriptomicsMagnaporthe oryzaePlant surfacesFusarium graminearumF. graminearumGene expressionPlant pathogensAppressorium formationFungal plant pathogensComparative gene expressionBiosynthesis of deoxynivalenolHost-pathogen interfaceTrichothecene genesTrichome basesLaser dissection microscopyM. oryzaeFungal ingressTranscriptomic analysisInfection strategiesHelp of enzymesPlant cuticlesSpore germlingsTranscriptomicsMode of penetrationResistant cultivars
2022
Transcriptional Divergence Underpinning Sexual Development in the Fungal Class Sordariomycetes
Kim W, Wang Z, Kim H, Pham K, Tu Y, Townsend JP, Trail F. Transcriptional Divergence Underpinning Sexual Development in the Fungal Class Sordariomycetes. MBio 2022, 13: e01100-22. PMID: 35638737, PMCID: PMC9239162, DOI: 10.1128/mbio.01100-22.Peer-Reviewed Original ResearchMeSH KeywordsFruiting Bodies, FungalFungal ProteinsGene Expression Regulation, FungalNeurospora crassaSexual DevelopmentTranscriptomeConceptsSingle-copy orthologous genesFungal class SordariomycetesTranscriptional divergenceOrthologous genesHypothetical proteinsNovel genesPerithecial developmentTranscriptional activationClass SordariomycetesGene expressionRich genomic resourceGene expression divergenceMulticellular fruiting bodiesBody developmentSuccessful sexual reproductionKey developmental genesSpecies-specific functionsFunctional protein domainsKnockout of genesRecent common ancestorGene expression levelsOrthologous counterpartsSordariomycetes speciesDevelopmental transcriptomeExpression divergence
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 history
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
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 specificityPhylogenetic and phylogenomic overview of the Polyporales
Binder M, Justo A, Riley R, Salamov A, Lopez-Giraldez F, Sjökvist E, Copeland A, Foster B, Sun H, Larsson E, Larsson KH, Townsend J, Grigoriev IV, Hibbett DS. Phylogenetic and phylogenomic overview of the Polyporales. Mycologia 2013, 105: 1350-1373. PMID: 23935031, DOI: 10.3852/13-003.Peer-Reviewed Original ResearchConceptsSingle-copy genePhylogenetic informativeness analysesResidual polyporoid cladeBayesian phylogenetic analysisPolyporales speciesMajor lineagesPhylogenomic datasetsAvailable genomesCorresponding cladesPhlebioid cladePolyporoid cladeNew genomesGenome dataPhylogenetic analysisSuprageneric taxonomyCertain taxaPhylogenetic systematicsGenomic datasetsIdentical topologiesPolyporalesGenomeCladeSupport valuesGenesLineages
2011
Getting the Most Out of Your Fungal Microarray Data: Two Cost- and Time-Effective Methods
Mathioni SM, Beló A, Townsend JP, Donofrio NM. Getting the Most Out of Your Fungal Microarray Data: Two Cost- and Time-Effective Methods. Methods In Molecular Biology 2011, 722: 61-77. PMID: 21590413, DOI: 10.1007/978-1-61779-040-9_5.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsExpensive softwareData generationMultiple platformsGenomic data generationEfficient waySuch dataPossible informationGenome sequencing technologiesKind of analysisData analysisFungal dataUsersDifferent environmentsMicroarray dataBioinformaticistsCostExperimental costSoftwareProtocolBottleneckPlatformTaskTechnologyDataAcademia
2003
Population Genetic Variation in Genome-Wide Gene Expression
Townsend JP, Cavalieri D, Hartl DL. Population Genetic Variation in Genome-Wide Gene Expression. Molecular Biology And Evolution 2003, 20: 955-963. PMID: 12716989, DOI: 10.1093/molbev/msg106.Peer-Reviewed Original ResearchConceptsGene expression levelsGene expressionNatural populationsGenetic variationNatural isolatesExpression levelsGenome-wide gene expressionPopulation genetic variationGenome-wide scaleComparative gene expressionDifferential gene expressionDNA microarray technologyAmino acid metabolismWine yeast SaccharomycesSulfur assimilationEvolutionary biologistsGenomic scaleYeast SaccharomycesNatural selectionS. cerevisiaeProtein degradationSuch traitsDifferential reproductionMicroarray technologyOrganic evolution