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
2020
Unmatched Level of Molecular Convergence among Deeply Divergent Complex Multicellular Fungi
Merényi Z, Prasanna AN, Wang Z, Kovács K, Hegedüs B, Bálint B, Papp B, Townsend JP, Nagy LG. Unmatched Level of Molecular Convergence among Deeply Divergent Complex Multicellular Fungi. Molecular Biology And Evolution 2020, 37: 2228-2240. PMID: 32191325, PMCID: PMC7403615, DOI: 10.1093/molbev/msaa077.Peer-Reviewed Original ResearchMeSH KeywordsAscomycotaBasidiomycotaBiological EvolutionFruiting Bodies, FungalGene Expression Regulation, DevelopmentalMultigene FamilyConceptsComplex multicellularityGene familyMulticellular fruiting bodiesGene family levelLarge phylogenetic distancesSimilar selection pressuresRecent common ancestorFungal ancestorsFungal genomesGenomic repertoireMolecular convergenceMulticellular fungiPhylogenetic distanceConvergent evolutionEvolutionary convergenceLarge cladeEvolutionary trajectoriesCommon ancestorIndependent evolutionNatural selectionSelection pressureEvolutionary predispositionMulticellularityCladeFruiting bodies
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 ResearchMeSH KeywordsExoribonucleasesFruiting Bodies, FungalFusariumGene Expression ProfilingGene Expression Regulation, FungalRNA StabilityRNA, AntisenseRNA, Long NoncodingConceptsSmall 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
The ancestral levels of transcription and the evolution of sexual phenotypes in filamentous fungi
Trail F, Wang Z, Stefanko K, Cubba C, Townsend JP. The ancestral levels of transcription and the evolution of sexual phenotypes in filamentous fungi. PLOS Genetics 2017, 13: e1006867. PMID: 28704372, PMCID: PMC5509106, DOI: 10.1371/journal.pgen.1006867.Peer-Reviewed Original ResearchConceptsGene expressionFilamentous fungiCommon garden environmentBody developmentWide gene expressionGene expression phenotypesGene deletion studiesGene expression measurementsMulticellular developmentDivergent speciesSexual phenotypeGene familyEvolved increasesDivergent morphologyKnockout phenotypesAncestral levelsWhole genomeGarden environmentExpression phenotypesDeletion studiesRelevant genesPhenotypic analysisDevelopmental stagesExpression measurementsBody morphology
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
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