A Robust Phylogenomic Time Tree for Biotechnologically and Medically Important Fungi in the Genera Aspergillus and Penicillium
出版年份 2019 全文链接
标题
A Robust Phylogenomic Time Tree for Biotechnologically and Medically Important Fungi in the Genera Aspergillus and Penicillium
作者
关键词
-
出版物
mBio
Volume 10, Issue 4, Pages -
出版商
American Society for Microbiology
发表日期
2019-07-08
DOI
10.1128/mbio.00925-19
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- Characterizing the Pathogenic, Genomic, and Chemical Traits of Aspergillus fischeri, a Close Relative of the Major Human Fungal Pathogen Aspergillus fumigatus
- (2019) Matthew E. Mead et al. mSphere
- Linking secondary metabolites to gene clusters through genome sequencing of six diverseAspergillusspecies
- (2018) Inge Kjærbølling et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The birth, evolution and death of metabolic gene clusters in fungi
- (2018) Antonis Rokas et al. NATURE REVIEWS MICROBIOLOGY
- Systematic Dissection of the Evolutionarily Conserved WetA Developmental Regulator across a Genus of Filamentous Fungi
- (2018) Ming-Yueh Wu et al. mBio
- Tempo and Mode of Genome Evolution in the Budding Yeast Subphylum
- (2018) Xing-Xing Shen et al. CELL
- Genomic features of the damselfly Calopteryx splendens representing a sister clade to most insect orders
- (2017) Panagiotis Ioannidis et al. Genome Biology and Evolution
- UFBoot2: Improving the Ultrafast Bootstrap Approximation
- (2017) Diep Thi Hoang et al. MOLECULAR BIOLOGY AND EVOLUTION
- Evaluating Fast Maximum Likelihood-Based Phylogenetic Programs Using Empirical Phylogenomic Data Sets
- (2017) Xiaofan Zhou et al. MOLECULAR BIOLOGY AND EVOLUTION
- BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics
- (2017) Robert M Waterhouse et al. MOLECULAR BIOLOGY AND EVOLUTION
- ModelFinder: fast model selection for accurate phylogenetic estimates
- (2017) Subha Kalyaanamoorthy et al. NATURE METHODS
- Genomic evidence reveals a radiation of placental mammals uninterrupted by the KPg boundary
- (2017) Liang Liu et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation
- (2017) Huai-Chun Wang et al. SYSTEMATIC BIOLOGY
- Global analysis of biosynthetic gene clusters reveals vast potential of secondary metabolite production in Penicillium species
- (2017) Jens Christian Nielsen et al. Nature Microbiology
- Contentious relationships in phylogenomic studies can be driven by a handful of genes
- (2017) Xing-Xing Shen et al. Nature Ecology & Evolution
- Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life
- (2017) Dahiana Arcila et al. Nature Ecology & Evolution
- Regulation and Role of Fungal Secondary Metabolites
- (2016) Juliane Macheleidt et al. Annual Review of Genetics
- A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference
- (2016) Xing-Xing Shen et al. Genome Biology and Evolution
- Computing the Internode Certainty and Related Measures from Partial Gene Trees
- (2016) Kassian Kobert et al. MOLECULAR BIOLOGY AND EVOLUTION
- New sections in Penicillium containing novel species producing patulin, pyripyropens or other bioactive compounds
- (2016) J. Houbraken et al. PERSOONIA
- Aspergillus is monophyletic: Evidence from multiple gene phylogenies and extrolites profiles
- (2016) S. Kocsubé et al. STUDIES IN MYCOLOGY
- Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices
- (2016) Olga Chernomor et al. SYSTEMATIC BIOLOGY
- Choosing one name for pleomorphic fungi: The example of Aspergillus versus Eurotium, Neosartorya and Emericella
- (2016) John W. Taylor et al. TAXON
- The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves
- (2016) Alexander Suh ZOOLOGICA SCRIPTA
- in silico Whole Genome Sequencer & Analyzer (iWGS): A Computational Pipeline to Guide the Design and Analysis of de novo Genome Sequencing Studies
- (2016) X. Zhou et al. G3-Genes Genomes Genetics
- Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data
- (2016) Xing-Xing Shen et al. G3-Genes Genomes Genetics
- Genome Sequencing and Comparative Genomics Analysis Revealed Pathogenic Potential in Penicillium capsulatum as a Novel Fungal Pathogen Belonging to Eurotiales
- (2016) Ying Yang et al. Frontiers in Microbiology
- Chemodiversity in the genus Aspergillus
- (2015) Jens C. Frisvad et al. APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
- ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes
- (2015) Siavash Mirarab et al. BIOINFORMATICS
- Genomic Analysis of an Ascomycete Fungus from the Rice Planthopper Reveals How It Adapts to an Endosymbiotic Lifestyle
- (2015) Hai-Wei Fan et al. Genome Biology and Evolution
- Genome, Transcriptome, and Functional Analyses ofPenicillium expansumProvide New Insights Into Secondary Metabolism and Pathogenicity
- (2015) Ana-Rosa Ballester et al. MOLECULAR PLANT-MICROBE INTERACTIONS
- Genomic Characterization Reveals Insights Into Patulin Biosynthesis and Pathogenicity in Penicillium Species
- (2015) Boqiang Li et al. MOLECULAR PLANT-MICROBE INTERACTIONS
- The adaptive radiation of lichen-forming Teloschistaceae is associated with sunscreening pigments and a bark-to-rock substrate shift
- (2015) Ester Gaya et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference
- (2015) Ge Tan et al. SYSTEMATIC BIOLOGY
- FactoMineR: AnRPackage for Multivariate Analysis
- (2015) Sébastien Lê et al. Journal of Statistical Software
- RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
- (2014) Alexandros Stamatakis BIOINFORMATICS
- Novel Information Theory-Based Measures for Quantifying Incongruence among Phylogenetic Trees
- (2014) Leonidas Salichos et al. MOLECULAR BIOLOGY AND EVOLUTION
- IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies
- (2014) Lam-Tung Nguyen et al. MOLECULAR BIOLOGY AND EVOLUTION
- Estimating the Phanerozoic history of the Ascomycota lineages: Combining fossil and molecular data
- (2014) Christina Beimforde et al. MOLECULAR PHYLOGENETICS AND EVOLUTION
- Aspergillus, its sexual states and the new International Code of Nomenclature
- (2014) John I. Pitt et al. MYCOLOGIA
- strap: an R package for plotting phylogenies against stratigraphy and assessing their stratigraphic congruence
- (2014) Mark A. Bell et al. PALAEONTOLOGY
- Phylogeny, identification and nomenclature of the genus Aspergillus
- (2014) R.A. Samson et al. STUDIES IN MYCOLOGY
- Spearman's rank correlation coefficient
- (2014) P. Sedgwick BMJ-British Medical Journal
- Sexual Reproduction of Human Fungal Pathogens
- (2014) J. Heitman et al. Cold Spring Harbor Perspectives in Medicine
- FusariumPathogenomics
- (2013) Li-Jun Ma et al. Annual Review of Microbiology
- QUAST: quality assessment tool for genome assemblies
- (2013) Alexey Gurevich et al. BIOINFORMATICS
- Informed and automated k-mer size selection for genome assembly
- (2013) R. Chikhi et al. BIOINFORMATICS
- Gene make-up: rapid and massive intron gains after horizontal transfer of a bacterial α-amylase gene to Basidiomycetes
- (2013) Jean-Luc Da Lage et al. BMC EVOLUTIONARY BIOLOGY
- Phylogenetic analyses of RPB1 and RPB2 support a middle Cretaceous origin for a clade comprising all agriculturally and medically important fusaria
- (2013) Kerry O’Donnell et al. FUNGAL GENETICS AND BIOLOGY
- Genome-wide evidence for speciation with gene flow inHeliconiusbutterflies
- (2013) Simon H. Martin et al. GENOME RESEARCH
- MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
- (2013) K. Katoh et al. MOLECULAR BIOLOGY AND EVOLUTION
- Inferring ancient divergences requires genes with strong phylogenetic signals
- (2013) Leonidas Salichos et al. NATURE
- Sexual reproduction and mating-type–mediated strain development in the penicillin-producing fungusPenicillium chrysogenum
- (2013) Julia Böhm et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Origin of land plants using the multispecies coalescent model
- (2013) Bojian Zhong et al. TRENDS IN PLANT SCIENCE
- The Composition of Camembert Cheese-Ripening Cultures Modulates both Mycelial Growth and Appearance
- (2012) Marie-Hélène Lessard et al. APPLIED AND ENVIRONMENTAL MICROBIOLOGY
- Genome sequence of the necrotrophic fungus Penicillium digitatum, the main postharvest pathogen of citrus
- (2012) Marina Marcet-Houben et al. BMC GENOMICS
- The Evolutionary Imprint of Domestication on Genome Variation and Function of the Filamentous Fungus Aspergillus oryzae
- (2012) John G. Gibbons et al. CURRENT BIOLOGY
- A taxonomic and ecological overview of cheese fungi
- (2012) Jeanne Ropars et al. INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
- Molecular Epidemiology of Aspergillus fumigatus Isolates Harboring the TR34/L98H Azole Resistance Mechanism
- (2012) S. M. T. Camps et al. JOURNAL OF CLINICAL MICROBIOLOGY
- SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing
- (2012) Anton Bankevich et al. JOURNAL OF COMPUTATIONAL BIOLOGY
- OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs
- (2012) Robert M. Waterhouse et al. NUCLEIC ACIDS RESEARCH
- Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model
- (2012) S. Song et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The function and evolution of the Aspergillus genome
- (2012) John G. Gibbons et al. TRENDS IN MICROBIOLOGY
- The unbearable uncertainty of Bayesian divergence time estimation
- (2012) Mario DOS REIS et al. Journal of Systematics and Evolution
- The impact of taxon sampling on phylogenetic inference: a review of two decades of controversy
- (2011) A. R. Nabhan et al. BRIEFINGS IN BIOINFORMATICS
- A ‘missing’ family of classical orthogonal polynomials
- (2011) Luc Vinet et al. Journal of Physics A-Mathematical and Theoretical
- Statistics and Truth in Phylogenomics
- (2011) S. Kumar et al. MOLECULAR BIOLOGY AND EVOLUTION
- Addressing Inter-Gene Heterogeneity in Maximum Likelihood Phylogenomic Analysis: Yeasts Revisited
- (2011) Jaqueline Hess et al. PLoS One
- Phylogeny of Penicillium and the segregation of Trichocomaceae into three families
- (2011) J. Houbraken et al. STUDIES IN MYCOLOGY
- Accelerated Profile HMM Searches
- (2011) Sean R. Eddy PLoS Computational Biology
- The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell
- (2010) T. Junier et al. BIOINFORMATICS
- BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments
- (2010) Alexis Criscuolo et al. BMC EVOLUTIONARY BIOLOGY
- The hearing gene Prestin unites echolocating bats and whales
- (2010) Ying Li et al. CURRENT BIOLOGY
- Fungal secondary metabolites as modulators of interactions with insects and other arthropods
- (2010) Marko Rohlfs et al. FUNGAL GENETICS AND BIOLOGY
- A historical perspective on the discovery of statins
- (2010) Akira ENDO PROCEEDINGS OF THE JAPAN ACADEMY SERIES B-PHYSICAL AND BIOLOGICAL SCIENCES
- A Brief History of the Antibiotic Era: Lessons Learned and Challenges for the Future
- (2010) Rustam I. Aminov Frontiers in Microbiology
- trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
- (2009) S. Capella-Gutierrez et al. BIOINFORMATICS
- Biopython: freely available Python tools for computational molecular biology and bioinformatics
- (2009) P. J. A. Cock et al. BIOINFORMATICS
- BLAST+: architecture and applications
- (2009) Christiam Camacho et al. BMC BIOINFORMATICS
- Phylogenomics Revives Traditional Views on Deep Animal Relationships
- (2009) Hervé Philippe et al. CURRENT BIOLOGY
- Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives
- (2009) T. J. Sharpton et al. GENOME RESEARCH
- Microsatellite loci to recognize species for the cheese starter and contaminating strains associated with cheese manufacturing
- (2009) Frédéric Giraud et al. INTERNATIONAL JOURNAL OF FOOD MICROBIOLOGY
- Evidence for an ancient adaptive episode of convergent molecular evolution
- (2009) T. A. Castoe et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Empirical profile mixture models for phylogenetic reconstruction
- (2008) Le Si Quang et al. BIOINFORMATICS
- Database indexing for production MegaBLAST searches
- (2008) Aleksandr Morgulis et al. BIOINFORMATICS
- Secondary metabolism: regulation and role in fungal biology
- (2008) Ellen M Fox et al. CURRENT OPINION IN MICROBIOLOGY
- Genomics of Aspergillus oryzae: Learning from the History of Koji Mold and Exploration of Its Future
- (2008) M. Machida et al. DNA RESEARCH
- IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?
- (2008) Scott V. Edwards EVOLUTION
- An Improved General Amino Acid Replacement Matrix
- (2008) S. Q. Le et al. MOLECULAR BIOLOGY AND EVOLUTION
- Database resources of the National Center for Biotechnology Information
- (2008) E. W. Sayers et al. NUCLEIC ACIDS RESEARCH
- Conservation of divergent transcription in fungi
- (2008) Philip R. Kensche et al. TRENDS IN GENETICS
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started