Featured Publications
Metabolism 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 switchSex-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 specificity
2023
Chapter 5 Measurement and meaning in gene expression evolution
Diaz R, Wang Z, Townsend J. Chapter 5 Measurement and meaning in gene expression evolution. 2023, 111-129. DOI: 10.1016/b978-0-323-91810-7.00008-x.ChaptersGene expressionPhenotypic evolutionGene expression evolutionMessenger RNAEffects of epistasisIndividual gene expressionRibonucleic acid sequencingExpression evolutionNonmodel speciesFunctional genomicsGenomic scaleTranscriptional networksGene functionRelative mRNA abundancePhenotypic variationPopulation geneticsReference genomeTranscriptome profilingBiological traitsMolecular adjustmentsQuantitative traitsPhenotypic varianceGene interactionsGenetic controlExpression variation
2022
Placing human gene families into their evolutionary context
Dornburg A, Mallik R, Wang Z, Bernal M, Thompson B, Bruford E, Nebert D, Vasiliou V, Yohe L, Yoder J, Townsend J. Placing human gene families into their evolutionary context. Human Genomics 2022, 16: 56. PMID: 36369063, PMCID: PMC9652883, DOI: 10.1186/s40246-022-00429-5.Peer-Reviewed Original ResearchConceptsHuman gene familyGene familyHuman genomeEvolutionary contextGene family evolutionNon-model organismsFirst human genomeGenome biologyComparative genomicsFamily evolutionDistant speciesDraft sequenceGenomic studiesGene expressionGenome sequencingSequence complexityGenomeCancer biologyUnprecedented insightsNovel discoveriesCritical roleOrganismsBiologyComparative approachFamilyTranscriptional 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 ResearchConceptsSingle-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