2022
Differential 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 progression
2013
Complete Mitochondrial Genomes of Ancient Canids Suggest a European Origin of Domestic Dogs
Thalmann O, Shapiro B, Cui P, Schuenemann VJ, Sawyer SK, Greenfield DL, Germonpré MB, Sablin MV, López-Giráldez F, Domingo-Roura X, Napierala H, Uerpmann HP, Loponte DM, Acosta AA, Giemsch L, Schmitz RW, Worthington B, Buikstra JE, Druzhkova A, Graphodatsky AS, Ovodov ND, Wahlberg N, Freedman AH, Schweizer RM, Koepfli K, Leonard JA, Meyer M, Krause J, Pääbo S, Green RE, Wayne RK. Complete Mitochondrial Genomes of Ancient Canids Suggest a European Origin of Domestic Dogs. Science 2013, 342: 871-874. PMID: 24233726, DOI: 10.1126/science.1243650.Peer-Reviewed Original ResearchConceptsModern dogsMitochondrial genomeOnset of domesticationPrehistoric canidsAncient canidsComplete mitochondrial genomeModern canidsNew WorldDomestic dogsEast AsiaEuropean originDomestication processMolecular datingGenetic dataEuropeGenomeTemporal originCanidsDatingEurasiaCulminationSiberiaAsiaOriginDomesticationPhylogenetic 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
Assessing the Role of Tandem Repeats in Shaping the Genomic Architecture of Great Apes
Farré M, Bosch M, López-Giráldez F, Ponsà M, Ruiz-Herrera A. Assessing the Role of Tandem Repeats in Shaping the Genomic Architecture of Great Apes. PLOS ONE 2011, 6: e27239. PMID: 22076140, PMCID: PMC3208591, DOI: 10.1371/journal.pone.0027239.Peer-Reviewed Original ResearchConceptsEvolutionary breakpoint regionsTandem repeatsEvolutionary regionBreakpoint regionSpecific tandem repeatMore base pairsGreat apesGenome architectureMammalian genomesGenome organizationSynteny blocksChromatin conformationEvolutionary biologistsGenomic architectureAncestral reconstructionGenome instabilityMacaque genomeChromosomal reorganizationTransposable elementsGenomic regionsHuman genomeGenomic areasAlu elementsGenomeBase pairsPhyDesign: 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