Phylogenomic analyses support the monophyly of Taphrinomycotina, including Schizosaccharomyces fission yeasts.

No abstract is available for this paper.

• Publication year

  2008

• Venue

  Molecular biology and evolution

• Publication date

  2008-10-14

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1093/molbev/msn221PMID 18922765PMCID PMC8929177
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Construction of cDNA libraries: focus on protists and fungi.

  2009cited by this paper
• Sequencing complete mitochondrial and plastid genomes

  2007cited by this paper
• TBestDB: a taxonomically broad database of expressed sequence tags (ESTs)

  2007cited by this paper
• Toward resolving the eukaryotic tree: the phylogenetic positions of jakobids and cercozoans.

  2007cited by this paper
• Assessment of phylogenomic and orthology approaches for phylogenetic inference

  2007cited by this paper
• Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model

  2007cited by this paper
• BMC Evolutionary Biology BioMed Central Research article

  2007cited by this paper
• Purification of mitochondrial and plastid DNA

  2007cited by this paper
• SCaFoS: a tool for Selection, Concatenation and Fusion of Sequences for phylogenomics

  2007cited by this paper
• The mitochondrial genome of the wine yeast Hanseniaspora uvarum: a unique genome organization among yeast/fungal counterparts.

  2006cited by this paper
• Loss of the flagellum happened only once in the fungal lineage: phylogenetic structure of Kingdom Fungi inferred from RNA polymerase II subunit genes

  2006cited by this paper
• A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis

  2006cited by this paper
• Reconstructing the early evolution of Fungi using a six-gene phylogeny

  2006cited by this paper
• Early diverging Ascomycota: phylogenetic divergence and related evolutionary enigmas.

  2006cited by this paper
• A phylogenomic analysis of the Ascomycota.

  2006cited by this paper
• A five-gene phylogeny of Pezizomycotina.

  2006cited by this paper
• RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models

  2006influential reference
• Phylogenomics and the reconstruction of the tree of life

  2005cited by this paper
• AutoFACT: An Automatic Functional Annotation and Classification Tool

  2005cited by this paper
• Bayesian and maximum likelihood phylogenetic analyses of protein sequence data under relative branch-length differences and model violation

  2005cited by this paper
• A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process.

  2004cited by this paper
• MUSCLE: a multiple sequence alignment method with reduced time and space complexity

  2004cited by this paper
• An assessment of accuracy, error, and conflict with support values from genome-scale phylogenetic data.

  2004cited by this paper
• PAUP* [Phylogenetic Analysis Using Parsimony (and Other Methods)]

  2004cited by this paper
• Phylogenomics of eukaryotes: impact of missing data on large alignments.

  2004cited by this paper
• Phylogeny and Evolution of Medical Species of Candida and Related Taxa: a Multigenic Analysis

  2004cited by this paper
• Evolution of monoblepharidalean fungi based on complete mitochondrial genome sequences.

  2003cited by this paper
• MrBayes 3: Bayesian phylogenetic inference under mixed models

  2003influential reference
• Missing data, incomplete taxa, and phylogenetic accuracy.

  2003cited by this paper
• A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.

  2003cited by this paper
• Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics.

  2003cited by this paper
• Obtaining maximal concatenated phylogenetic data sets from large sequence databases.

  2003cited by this paper
• Handbook of fungal biotechnology

  2003cited by this paper
• Fungal Evolution Meets Fungal Genomics

  2003influential reference
• TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing

  2002cited by this paper
• The closest unicellular relatives of animals.

  2002cited by this paper
• An approximately unbiased test of phylogenetic tree selection.

  2002cited by this paper
• CONSEL: for assessing the confidence of phylogenetic tree selection

  2001cited by this paper
• New center a stroke of gene-ius.

  2001cited by this paper
• The phylogenetic trunk: maximal inclusion of taxa with missing data in an analysis of the lepospondyli (Vertebrata, Tetrapoda).

  2001cited by this paper
• A kingdom-level phylogeny of eukaryotes based on combined protein data.

  2000cited by this paper
• Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis.

  2000cited by this paper
• Archaea sister group of Bacteria? Indications from tree reconstruction artifacts in ancient phylogenies.

  1999cited by this paper
• Phylogenetic relationships among Taphrina, Saitoella, and other higher fungi.

  1993cited by this paper
• Ribosomal RNA sequence shows Pneumocystis carinii to be a member of the Fungi

  1988cited by this paper
• Non-commercial Research and Educational Use including without Limitation Use in Instruction at Your Institution, Sending It to Specific Colleagues That You Know, and Providing a Copy to Your Institution's Administrator. All Other Uses, Reproduction and Distribution, including without Limitation Comm

  year unknowncited by this paper

• Evolving Spectrum of Pneumocystis Host Specificity, Genetic Diversity, and Evolution.

  2025cites this paper
• Golgi_traff phylogeny reveals ancient eukaryotic genes with recent surprises: replication and diversification of HID1 domain-containing protein unique to Schizosaccharomyces

  2025cites this paper
• Exploring criteria for constructing suprageneric classifications of fungi in the genomic era: a case study of suborders Agaricineae, Pluteineae, and Tricholomatineae (Agaricales)

  2025cites this paper
• Retracing the evolution of Pneumocystis species, with a focus on the human pathogen Pneumocystis jirovecii

  2024influential citation
• Classes and phyla of the kingdom Fungi

  2024cites this paper
• Understanding the molecular mechanisms of human diseases: the benefits of fission yeasts.

  2024cites this paper
• Reinstatement of the fission yeast species Schizosaccharomyces versatilis Wickerham et Duprat, a sibling species of Schizosaccharomyces japonicus

  2024cites this paper
• Digital finance and carbon emissions: empirical evidence from China

  2023cites this paper
• Schizosaccharomyces versatilis represents a distinct evolutionary lineage

  2023cites this paper
• The Electricity Rebound Effect: Empirical Evidence From the Chinese Chemical Industry

  2022cites this paper
• A high-quality reference genome for the fission yeast Schizosaccharomyces osmophilus

  2022influential citation
• Identifying and Regulating the Environmental Risks in the Development and Utilization of Natural Gas as a Low-Carbon Energy Source

  2021cites this paper
• Characterization of mitogenomes from four Mucorales species and insights into pathogenicity

  2021cites this paper
• Novakomyces olei sp. nov., the First Member of a Novel Taphrinomycotina Lineage

  2021cites this paper
• Genome Comparisons of the Fission Yeasts Reveal Ancient Collinear Loci Maintained by Natural Selection

  2021cites this paper
• Effects of benzo[a]pyrene toxicity on morphology and ultrastructure of Hordeum sativum

  2020cites this paper
• An Overview of Genomics, Phylogenomics and Proteomics Approaches in Ascomycota

  2020cites this paper
• A novel Arabidopsis phyllosphere resident Protomyces species and a re-examination of genus Protomyces based on genome sequence data

  2019cites this paper
• Mancha gris de la hoja del tomate: identificación, biología y genómica del agente etiológico

  2019cites this paper
• Intraspecific Diversity of Fission Yeast Mitochondrial Genomes

  2019cites this paper
• Lipolytic Enzymes with Hydrolytic and Esterification Activities Produced by Filamentous Fungi Isolated from Decomposition Leaves in an Aquatic Environment

  2019cites this paper
• Fungal evolution: diversity, taxonomy and phylogeny of the Fungi

  2019influential citation
• Phylogenomic analysis of 2556 single-copy protein-coding genes resolves most evolutionary relationships for the major clades in the most diverse group of lichen-forming fungi

  2018cites this paper
• Phylogenetic taxon definitions for Fungi, Dikarya, Ascomycota and Basidiomycota

  2018cites this paper
• Production of exopolysaccharide by strains of Lactobacillus plantarum YO175 and OF101 isolated from traditional fermented cereal beverage

  2018cites this paper
• Genomics and evolution of Pneumocystis species.

  2018cites this paper
• Detection of Pneumocystis jirovecii by nested PCR in HIV-negative patients with pulmonary disease.

  2017cites this paper
• The mitochondrial genome of the plant-pathogenic fungus Stemphylium lycopersici uncovers a dynamic structure due to repetitive and mobile elements

  2017cites this paper
• Changes in nucleosome formation at gene promoters in the archiascomycetous yeast Saitoella complicata

  2017cites this paper
• Advances in Fungal Phylogenomics and Their Impact on Fungal Systematics.

  2017cites this paper
• A Distance Measure for Building Phylogenetic Trees: A First Approach

  2017cites this paper
• A Survey of the Gene Repertoire of Gigaspora rosea Unravels Conserved Features among Glomeromycota for Obligate Biotrophy

  2016influential citation
• Scaling up discovery of hidden diversity in fungi: impacts of barcoding approaches

  2016cites this paper
• Phylogenetic Resolution of Deep Eukaryotic and Fungal Relationships Using Highly Conserved Low-Copy Nuclear Genes

  2016cites this paper
• Reconstructing the Backbone of the Saccharomycotina Yeast Phylogeny Using Genome-Scale Data

  2016cites this paper
• THE EFFECTS OF ANTI-CD20 THERAPY ON SUSCEPTIBILITY TO PNEUMOCYSTIS INFECTION AND THE CD4+ T-CELL SIGNALS THAT MEDIATE CLEARANCE

  2015cites this paper
• Draft Genome Sequence of the Archiascomycetous Yeast Saitoella complicata

  2015cites this paper
• Pondering Mating: Pneumocystis jirovecii, the Human Lung Pathogen, Selfs without Mating Type Switching, in Contrast to Its Close Relative Schizosaccharomyces pombe

  2015influential citation
• Mitochondrial genome evolution in yeasts: an all-encompassing view.

  2015cites this paper
• Relationship between chromosomal GC content and isoelectric points of histones in fungi.

  2015cites this paper
• Identification of food and beverage spoilage yeasts from DNA sequence analyses.

  2015cites this paper
• 1 Saccharomycotina0Saccharomycotina and Taphrinomycotina:0Taphrinomycotina The Yeasts and Yeastlike Fungi of the Ascomycota

  2015cites this paper
• Heterobasidion annosum sensu stricto Pathogenesis: Bioinformatic and Functional Study of Cerato-platanin Family Proteins

  2015cites this paper
• Université de Montréal-Thèse numérique

  2014cites this paper
• Archaeorhizomyces borealis sp. nov. and a sequence-based classification of related soil fungal species.

  2014cites this paper
• 3 Phylogenomics for the Study of Fungal Biology

  2014cites this paper
• Pneumocystis carinii Subtelomeres

  2014cites this paper
• Sequencing and comparison of the mitochondrial COI gene from isolates of Arbuscular Mycorrhizal Fungi belonging to Gigasporaceae and Glomeraceae families.

  2014cites this paper
• UBL1 of Fusarium verticillioides links the N-end rule pathway to extracellular sensing and plant pathogenesis.

  2014cites this paper
• Subtelomeres

  2014cites this paper
• Comparative Genomics of Pneumocystis Species Suggests the Absence of Genes for myo-Inositol Synthesis and Reliance on Inositol Transport and Metabolism

  2014cites this paper
• A dually located multi‐HMG‐box protein of Aspergillus nidulans has a crucial role in conidial and ascospore germination

  2014cites this paper
• The early diverging ascomycetous budding yeast Saitoella complicata has three histone deacetylases belonging to the Clr6, Hos2, and Rpd3 lineages.

  2014cites this paper
• Complementation of a manganese-dependent superoxide dismutase-deficient yeast strain with Pneumocystis carinii sod2 gene.

  2014cites this paper
• Use of gene sequence analyses and genome comparisons for yeast systematics.

  2014cites this paper
• Comparative Genomics of Taphrina Fungi Causing Varying Degrees of Tumorous Deformity in Plants

  2014cites this paper
• Toward genome-enabled mycology

  2013cites this paper
• Examining new phylogenetic markers to uncover the evolutionary history of early-diverging fungi: comparing MCM7, TSR1 and rRNA genes for single- and multi-gene analyses of the Kickxellomycotina

  2013cites this paper
• Alternative Splicing and Subfunctionalization Generates Functional Diversity in Fungal Proteomes

  2013cites this paper
• Genome Sequencing of the Plant Pathogen Taphrina deformans, the Causal Agent of Peach Leaf Curl

  2013cites this paper
• Non-host and induced resistance in the Taphrina- Arabidopsis model system

  2013cites this paper
• Distribution and bioinformatic analysis of the cerato-platanin protein family in Dikarya

  2013cites this paper
• Phylogenetics and Evolution of Virulence in the Kingdom Fungi

  2013cites this paper
• Phylogenomic Analyses of Nuclear Genes Reveal the Evolutionary Relationships within the BEP Clade and the Evidence of Positive Selection in Poaceae

  2013cites this paper
• Sequencing and characterization of the complete mitochondrial genomes of three Pneumocystis species provide new insights into divergence between human and rodent Pneumocystis

  2013cites this paper
• Relationships among genera of the Saccharomycotina (Ascomycota) from multigene phylogenetic analysis of type species.

  2013cites this paper
• Pneumocystis Molecular Phylogeny: A Way to Understand Both Pneumocystosis Natural History and Host Taxonomy

  2012cites this paper
• The common ancestral core of vertebrate and fungal telomerase RNAs

  2012cites this paper
• Phylogenetic reference data for systematics and phylotaxonomy of arbuscular mycorrhizal fungi from phylum to species level.

  2012cites this paper
• What the Genomics of Arbuscular Mycorrhizal Symbiosis Teaches Us about Root Development

  2012cites this paper
• Group I intron-mediated trans-splicing in mitochondria of Gigaspora rosea and a robust phylogenetic affiliation of arbuscular mycorrhizal fungi with Mortierellales.

  2012influential citation
• Hal: an Automated Pipeline for Phylogenetic Analyses of Genomic Data

  2011cites this paper
• Pneumocystis: from a doubtful unique entity to a group of highly diversified fungal species.

  2011cites this paper
• Draft genome sequencing of the enigmatic yeast Saitoella complicata.

  2011cites this paper
• Reconstructing the Fungal Tree of Life Using Phylogenomics and a Preliminary Investigation of the Distribution of Yeast Prion-Like Proteins in the Fungal Kingdom

  2011influential citation
• Genetic and antigenic diversity in Pneumocystis jirovecii

  2011cites this paper
• A Consistent Phylogenetic Backbone for the Fungi

  2011cites this paper
• Molecular phylogeny, taxonomy and evolution of arbuscular mycorrhizal fungi

  2011influential citation
• Understanding evolutionary history using molecular phylogenetics: From genes to genomes

  2011cites this paper
• Regulation of Stomatal Tropism and Infection by Light in Cercospora zeae-maydis: Evidence for Coordinated Host/Pathogen Responses to Photoperiod?

  2011cites this paper
• An unusual tRNAThr derived from tRNAHis reassigns in yeast mitochondria the CUN codons to threonine

  2011cites this paper
• Archaeorhizomycetes: Unearthing an Ancient Class of Ubiquitous Soil Fungi

  2011cites this paper
• Distribution of Introns in Fungal Histone Genes

  2011cites this paper
• Ploidy of Cell-Sorted Trophic and Cystic Forms of Pneumocystis carinii

  2011cites this paper
• Pneumocystis carinii expresses an active Rtt109 histone acetyltransferase.

  2011cites this paper
• A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi

  2011cites this paper
• Identification and analysis of candidate fungal tRNA 3'-end processing endonucleases tRNase Zs, homologs of the putative prostate cancer susceptibility protein ELAC2

  2010cites this paper
• Phylogenetics and Phylogenomics of the Fungal Tree of Life

  2010cites this paper
• Conservation, duplication, and loss of the Tor signaling pathway in the fungal kingdom

  2010cites this paper
• Fungal phylogenomics.A global analysis of fungal genomes and their evolution

  2010cites this paper
• A stable backbone for the fungi

  2009cites this paper
• The mitochondrial genome sequence of the arbuscular mycorrhizal fungus Glomus intraradices isolate 494 and implications for the phylogenetic placement of Glomus.

  2009influential citation
• Misinformation about Pneumocystis

  2009cites this paper
• The search for the fungal tree of life.

  2009cites this paper
• Cyclostome and chondrichthyan adrenomedullins reveal ancestral features of the adrenomedullin family.

  2009cites this paper
• Phylogenomic analyses predict sistergroup relationship of nucleariids and Fungi and paraphyly of zygomycetes with significant support

  2009cites this paper
• The complete Glomus intraradices mitochondrial genome sequence--a milestone in mycorrhizal research.

  2009cites this paper
• Sequence and structure of the linear mitochondrial genome of Pneumocystis carinii

  2009cites this paper
• Geoglossomycetes cl. nov., Geoglossales ord. nov. and taxa above class rank in the Ascomycota Tree of Life

  2009cites this paper
• The Revision of Schizosaccharomycetaceae

  year unknowncites this paper