2015
Solving the ecological puzzle of mycorrhizal associations using data from annotated collections and environmental samples – an example of saddle fungi
Hwang J, Zhao Q, Yang ZL, Wang Z, Townsend JP. Solving the ecological puzzle of mycorrhizal associations using data from annotated collections and environmental samples – an example of saddle fungi. Environmental Microbiology Reports 2015, 7: 658-667. PMID: 26033481, DOI: 10.1111/1758-2229.12303.Peer-Reviewed Original ResearchConceptsPotential plant hostsEnvironmental sequencesDiversity of ecologyEctomycorrhizal fungiEcological roleGenetic divergenceGeographic distributionUnculturable fungiPhylogenetic informativenessPlant hostsEcologyITS phylogenyITS sequencesRoot tipsEnvironmental samplesSpeciesMetagenomic investigationSequence alignmentHost typeHelvellaDiversityFungiDiversity of relationshipsSequenceSoil
2014
Genome-Wide Characterization of Light-Regulated Genes in Neurospora crassa
Wu C, Yang F, Smith KM, Peterson M, Dekhang R, Zhang Y, Zucker J, Bredeweg EL, Mallappa C, Zhou X, Lyubetskaya A, Townsend JP, Galagan JE, Freitag M, Dunlap JC, Bell-Pedersen D, Sachs MS. Genome-Wide Characterization of Light-Regulated Genes in Neurospora crassa. G3: Genes, Genomes, Genetics 2014, 4: 1731-1745. PMID: 25053707, PMCID: PMC4169166, DOI: 10.1534/g3.114.012617.Peer-Reviewed Original ResearchConceptsNeurospora crassaRNA-seqFilamentous fungus Neurospora crassaGenome-wide characterizationProtein coding genesFungus Neurospora crassaPrevious microarray studyRibosome biogenesisCoding genesTranscriptional responseRRNA metabolismCellular metabolismMicroarray studiesGenesCrassaSignificant oxidative stressRNA levelsOrganismsMRNA levelsOxidative stressMRNAMetabolismBiogenesisTranscriptsMycelium
2012
Differential 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
Northern species of earth tongue genus Thuemenidium revisited, considering morphology, ecology and molecular phylogeny
Ohenoja E, Wang Z, Townsend JP, Mitchel D, Voitk A. Northern species of earth tongue genus Thuemenidium revisited, considering morphology, ecology and molecular phylogeny. Mycologia 2010, 102: 1089-1095. PMID: 20943508, DOI: 10.3852/09-317.Peer-Reviewed Original Research
2007
Enabling a Community to Dissect an Organism: Overview of the Neurospora Functional Genomics Project
Dunlap JC, Borkovich KA, Henn MR, Turner GE, Sachs MS, Glass NL, McCluskey K, Plamann M, Galagan JE, Birren BW, Weiss RL, Townsend JP, Loros JJ, Nelson MA, Lambreghts R, Colot HV, Park G, Collopy P, Ringelberg C, Crew C, Litvinkova L, DeCaprio D, Hood HM, Curilla S, Shi M, Crawford M, Koerhsen M, Montgomery P, Larson L, Pearson M, Kasuga T, Tian C, Baştürkmen M, Altamirano L, Xu J. Enabling a Community to Dissect an Organism: Overview of the Neurospora Functional Genomics Project. Advances In Genetics 2007, 57: 49-96. PMID: 17352902, PMCID: PMC3673015, DOI: 10.1016/s0065-2660(06)57002-6.Peer-Reviewed Original ResearchConceptsFunctional genomics projectsGenomics projectsFilamentous fungiFilamentous fungus NeurosporaFunctional genomic analysisNon-yeast fungiFunctional genomicsNeurospora genomeFungus NeurosporaNovel genesPositional cloningNeurospora crassaAntisense transcriptsGenomic analysisSNP mapAlternative promotersCDNA libraryExpression analysisGene replacementMutant strainSystematic disruptionExpression dataPhenotypic analysisNeurosporaConditions of growth
2005
Concerted Evolution in the Repeats of an Immunomodulating Cell Surface Protein, SOWgp, of the Human Pathogenic Fungi Coccidioides immitis and C. posadasii
Johannesson H, Townsend JP, Hung CY, Cole GT, Taylor JW. Concerted Evolution in the Repeats of an Immunomodulating Cell Surface Protein, SOWgp, of the Human Pathogenic Fungi Coccidioides immitis and C. posadasii. Genetics 2005, 171: 109-117. PMID: 15965255, PMCID: PMC1456504, DOI: 10.1534/genetics.105.040923.Peer-Reviewed Original ResearchMeSH KeywordsAntigens, FungalCoccidioidesCoccidioidomycosisDNA, FungalEvolution, MolecularGene ConversionGenetic VariationHumansMembrane GlycoproteinsMutationPhylogenyPolymorphism, GeneticRecombination, GeneticRepetitive Sequences, Nucleic AcidSequence Analysis, DNASpecies SpecificityTandem Repeat SequencesConceptsPathogenic fungus Coccidioides immitisConcerted evolutionProtein-coding genesC. posadasiiGenetic distance analysisPoint mutation rateHost-pathogen interactionsCell surface proteinsGenome dynamicsPathogen's benefitMultigene familyUnequal crossingGeographic rangeFungus Coccidioides immitisRepetitive domainEntire geneMutation rateRepetitive arraysSurface proteinsDistance analysisGenesHost immune systemImmune systemImmunodominant proteinsParasitic phase