2024
Corrigendum: The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomics
Wang Z, Kim W, Wang Y, Yakubovich E, Dong C, Trail F, Townsend J, Yarden O. Corrigendum: The Sordariomycetes: an expanding resource with Big Data for mining in evolutionary genomics and transcriptomics. Frontiers In Fungal Biology 2024, 5: 1478516. PMID: 39228963, PMCID: PMC11368851, DOI: 10.3389/ffunb.2024.1478516.Peer-Reviewed Original Research
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 approachFamilyDifferential Expression of Cell Wall Remodeling Genes Is Part of the Dynamic Phase-Specific Transcriptional Program of Conidial Germination of Trichoderma asperelloides
Gortikov M, Yakubovich E, Wang Z, López-Giráldez F, Tu Y, Townsend JP, Yarden O. Differential Expression of Cell Wall Remodeling Genes Is Part of the Dynamic Phase-Specific Transcriptional Program of Conidial Germination of Trichoderma asperelloides. Journal Of Fungi 2022, 8: 854. PMID: 36012842, PMCID: PMC9410309, DOI: 10.3390/jof8080854.Peer-Reviewed Original ResearchPolar growthTranscript abundanceConidial germinationGlucanase-encoding geneOnset of germinationTranscriptional hubsTranscriptional programsTrichoderma asperelloidesHyphal growthTranscriptional profilesDevelopmental eventsChitin synthaseHost recognitionDifferential expressionGerminationSpecific membersDormant conidiaFirst branchingGenomeGenesInitial branchingAbundanceNetwork analysisExpressionMorphological progressionSequencing and Analysis of the Entire Genome of the Mycoparasitic Bioeffector Fungus Trichoderma asperelloides Strain T 203 (Hypocreales)
Gortikov M, Wang Z, Steindorff AS, Grigoriev IV, Druzhinina IS, Townsend JP, Yarden O. Sequencing and Analysis of the Entire Genome of the Mycoparasitic Bioeffector Fungus Trichoderma asperelloides Strain T 203 (Hypocreales). Microbiology Resource Announcements 2022, 11: e00995-21. PMID: 35175124, PMCID: PMC8852338, DOI: 10.1128/mra.00995-21.Peer-Reviewed Original Research
2019
Comparative 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 development
2018
Neutral Theory and the Somatic Evolution of Cancer
Cannataro VL, Townsend JP. Neutral Theory and the Somatic Evolution of Cancer. Molecular Biology And Evolution 2018, 35: 1308-1315. PMID: 29684198, PMCID: PMC5967571, DOI: 10.1093/molbev/msy079.Peer-Reviewed Original Research
2017
Chapter One Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big Data
Dornburg A, Townsend JP, Wang Z. Chapter One Maximizing Power in Phylogenetics and Phylogenomics: A Perspective Illuminated by Fungal Big Data. Advances In Genetics 2017, 100: 1-47. PMID: 29153398, DOI: 10.1016/bs.adgen.2017.09.007.ChaptersConceptsTree of lifeFungal evolutionary biologyGenomic-scale dataHundreds of lociGenome-scale analysisFungal phylogenomicsFungal treeSpecies delimitationPhenotypic diversificationFirst genomeEvolutionary biologyPhylogenetic treePhylogenetic inferencePhylogenetic analysisEntire genomeTree inferenceReview of considerationsEvolutionary problemsPhylogenomicsGenomeTreesLociCentral roleExperimental designBiodiversity
2013
Phylogenetic 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 valuesGenesLineagesSex-linked transcriptional divergence in the hermaphrodite fungus Neurospora tetrasperma
Samils N, Gioti A, Karlsson M, Sun Y, Kasuga T, Bastiaans E, Wang Z, Li N, Townsend JP, Johannesson H. Sex-linked transcriptional divergence in the hermaphrodite fungus Neurospora tetrasperma. Proceedings Of The Royal Society B 2013, 280: 20130862. PMID: 23782882, PMCID: PMC3712418, DOI: 10.1098/rspb.2013.0862.Peer-Reviewed Original ResearchConceptsMating typesFilamentous ascomycete Neurospora tetraspermaNeurospora tetraspermaMating-type locusGene expression levelsExpression divergenceTranscriptional divergencePhenotypic divergenceFungal AnaloguesRecombinational suppressionMat ASequence divergenceN. tetraspermaMale developmentDivergent regionsFemale developmentMolecular phenotypesGenesSexual dimorphismMale tissuesExpression levelsDivergencePhenotypeAgar mediumGenome
2012
Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance
Zhang Z, Li J, Cui P, Ding F, Li A, Townsend JP, Yu J. Codon Deviation Coefficient: a novel measure for estimating codon usage bias and its statistical significance. BMC Bioinformatics 2012, 13: 43. PMID: 22435713, PMCID: PMC3368730, DOI: 10.1186/1471-2105-13-43.Peer-Reviewed Original ResearchConceptsCodon usage biasNucleotide compositionUsage biasGenome evolutionGene functionProtein functionCodon usageNatural selectionCodon positionsTranslational efficiencySelective pressureSequence compositionGene expressionSequence analysisSimulated sequencesSequenceGenomeGenesFundamental importanceMutationsInformative estimationExpression
2011
PhyDesign: an online application for profiling phylogenetic informativeness
López-Giráldez F, Townsend JP. PhyDesign: an online application for profiling phylogenetic informativeness. BMC Ecology And Evolution 2011, 11: 152. PMID: 21627831, PMCID: PMC3124428, DOI: 10.1186/1471-2148-11-152.Peer-Reviewed Original ResearchConceptsPhylogenetic informativenessPhylogenetic studiesPhylogenetic informativeness analysesBroad taxonomic samplingMolecular phylogenetic studiesTree of lifeOrthologous genesPhylogenetic samplingTaxonomic samplingPhylogenetic questionsPhylogenetic purposesEfficiency of sequencingSequence alignmentMarker selectionUltrametric treeDiverse suiteUtility of locusLociTreesUser-friendly toolGenomeGenesSequencingSpeciesDiversity
2006
Ecological and evolutionary genomics of Saccharomyces cerevisiae
LANDRY CR, TOWNSEND JP, HARTL DL, CAVALIERI D. Ecological and evolutionary genomics of Saccharomyces cerevisiae. Molecular Ecology 2006, 15: 575-591. PMID: 16499686, DOI: 10.1111/j.1365-294x.2006.02778.x.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsConceptsEvolutionary genomic studiesPrime model systemImportant genetic variationPowerful model speciesEvolutionary genomicsEvolutionary geneticsEvolutionary forcesFunctional genomicsYeast genomeNumerous habitatsModel speciesGenomic studiesUnicellular fungiGenetic variationBiology questionsS. cerevisiaeNatural isolatesGenetic levelGenomicsSaccharomycesModel systemYeastEukaryotesGenomeHabitats
2004
Gene expression profiling in evolutionary genetics
Hartl D, Meiklejohn C, Castillo-Davis C, Cavalieri D, Ranz J, Townsend J. Gene expression profiling in evolutionary genetics. 2004, 74-93. DOI: 10.1017/cbo9780511542619.007.Peer-Reviewed Reviews, Practice Guidelines, Standards, and Consensus StatementsNatural populationsPopulation geneticsKey model organismGenotypes of organismsGene expression profilingDNA sequencing strategyEvolutionary geneticsComparative genomicsEvolutionary timeModel organismsChain termination methodHuman genomePopulation geneticistsGenomic sequencesGenetic variationSingle speciesComplete sequenceExpression profilingMolecular geneticsGenetic differencesGenomeMolecular biologySequencing strategyMolecular levelDNA sequencing