Distinctive expansion of gene families associated with plant cell wall degradation, secondary metabolism, and nutrient uptake in the genomes of grapevine trunk pathogens

Molecular Polymorphism and Phenotypic Diversity in the Eutypa Dieback Pathogen Eutypa lata

(2015) Renaud Travadon et al.   PHYTOPATHOLOGY

Exploring genome characteristics and sequence quality without a reference

(2014) Jared T. Simpson   BIOINFORMATICS

Adaptive genomic structural variation in the grape powdery mildew pathogen, Erysiphe necator

(2014) Laura Jones et al.   BMC GENOMICS

fPoxDB: fungal peroxidase database for comparative genomics

(2014) Jaeyoung Choi et al.   BMC MICROBIOLOGY

Fungal model systems and the elucidation of pathogenicity determinants

(2014) Elena Perez-Nadales et al.   FUNGAL GENETICS AND BIOLOGY

Genomics of wood-degrading fungi

(2014) Robin A. Ohm et al.   FUNGAL GENETICS AND BIOLOGY

Fungal Cytochrome P450 Monooxygenases: Their Distribution, Structure, Functions, Family Expansion, and Evolutionary Origin

(2014) Wanping Chen et al.   Genome Biology and Evolution

Differential Production of Phytotoxins from Phomopsis sp. from Grapevine Plants Showing Esca Symptoms

(2014) Mary-Lorène Goddard et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Microbial genome-enabled insights into plant–microorganism interactions

(2014) David S. Guttman et al.   NATURE REVIEWS GENETICS

Trajectory and genomic determinants of fungal-pathogen speciation and host adaptation

(2014) Xiao Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi

(2014) Robert Riley et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Toxicity of extracellular proteins from Diplodia seriata and Neofusicoccum parvum involved in grapevine Botryosphaeria dieback

(2014) M. Bénard-Gellon et al.   PROTOPLASMA

Extensive Error in the Number of Genes Inferred from Draft Genome Assemblies

(2014) James F. Denton et al.   PLoS Computational Biology

Genome-wide transcriptional profiling of Botrytis cinerea genes targeting plant cell walls during infections of different hosts

(2014) Barbara Blanco-Ulate et al.   Frontiers in Plant Science

Can vessel dimension explain tolerance toward fungal vascular wilt diseases in woody plants? Lessons from Dutch elm disease and esca disease in grapevine

(2014) Jérôme Pouzoulet et al.   Frontiers in Plant Science

Expansion of the enzymatic repertoire of the CAZy database to integrate auxiliary redox enzymes

(2013) Anthony Levasseur et al.   Biotechnology for Biofuels

Comparative analysis of fungal genomes reveals different plant cell wall degrading capacity in fungi

(2013) Zhongtao Zhao et al.   BMC GENOMICS

Evolutionary dynamics of copy number variation in pig genomes in the context of adaptation and domestication

(2013) Yogesh Paudel et al.   BMC GENOMICS

Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici reveal polymorphic and haustorial expressed secreted proteins as candidate effectors

(2013) Dario Cantu et al.   BMC GENOMICS

Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3

(2013) Mira V. Han et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes

(2013) Pierre Gladieux et al.   MOLECULAR ECOLOGY

The Transporter Classification Database

(2013) Milton H. Saier et al.   NUCLEIC ACIDS RESEARCH

antiSMASH 2.0—a versatile platform for genome mining of secondary metabolite producers

(2013) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Susceptibility of Cultivated and Wild Vitis spp. to Wood Infection by Fungal Trunk Pathogens

(2013) Renaud Travadon et al.   PLANT DISEASE

Dating the Diversification of the Major Lineages of Ascomycota (Fungi)

(2013) María Prieto et al.   PLoS One

In search of solutions to grapevine trunk diseases through “crowd-sourced” science

(2013) Karen L. Block et al.   Frontiers in Plant Science

Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species

(2013) Keith R Bradnam et al.   GigaScience

Comparative genomics of the white-rot fungi, Phanerochaete carnosa and P. chrysosporium, to elucidate the genetic basis of the distinct wood types they colonize

(2012) Hitoshi Suzuki et al.   BMC GENOMICS

Systematic and searchable classification of cytochrome P450 proteins encoded by fungal and oomycete genomes

(2012) Venkatesh Moktali et al.   BMC GENOMICS

Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses

(2012) Richard J O'Connell et al.   NATURE GENETICS

Regulation of fungal secondary metabolism

(2012) Axel A. Brakhage   NATURE REVIEWS MICROBIOLOGY

A specialized ABC efflux transporter GcABC-G1 confers monoterpene resistance toGrosmannia clavigera, a bark beetle-associated fungal pathogen of pine trees

(2012) Ye Wang et al.   NEW PHYTOLOGIST

Grapevine trunk diseases: complex and still poorly understood

(2012) C. Bertsch et al.   PLANT PATHOLOGY

Unveiling the biosynthetic puzzle of destruxins in Metarhizium species

(2012) B. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Paleozoic Origin of Enzymatic Lignin Decomposition Reconstructed from 31 Fungal Genomes

(2012) D. Floudas et al.   SCIENCE

Identification, potential inoculum sources and pathogenicity of botryosphaeriaceous species associated with grapevine dieback disease in New Zealand

(2011) Nicholas T. Amponsah et al.   EUROPEAN JOURNAL OF PLANT PATHOLOGY

Oxidative Cleavage of Cellulose by Fungal Copper-Dependent Polysaccharide Monooxygenases

(2011) William T. Beeson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Grapevine powdery mildew (Erysiphe necator): a fascinating system for the study of the biology, ecology and epidemiology of an obligate biotroph

(2011) DAVID M. GADOURY et al.   MOLECULAR PLANT PATHOLOGY

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Obligate biotrophy features unraveled by the genomic analysis of rust fungi

(2011) S. Duplessis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Insights into the oxidative degradation of cellulose by a copper metalloenzyme that exploits biomass components

(2011) R. J. Quinlan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

Genomic Analysis of the Necrotrophic Fungal Pathogens Sclerotinia sclerotiorum and Botrytis cinerea

(2011) Joelle Amselem et al.   PLoS Genetics

Comparative Genomics Yields Insights into Niche Adaptation of Plant Vascular Wilt Pathogens

(2011) Steven J. Klosterman et al.   PLoS Pathogens

Phytotoxins Produced by Fungi Associated with Grapevine Trunk Diseases

(2011) Anna Andolfi et al.   Toxins

CAZymes Analysis Toolkit (CAT): Web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database

(2010) Byung H Park et al.   GLYCOBIOLOGY

Characterization of missing human genome sequences and copy-number polymorphic insertions

(2010) Jeffrey M Kidd et al.   NATURE METHODS

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

Inhibitory effects of polypeptides secreted by the grapevine pathogens Phaeomoniella chlamydospora and Phaeoacremonium aleophilum on plant cell activities

(2010) Estelle Luini et al.   PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Secondary metabolic gene clusters: evolutionary toolkits for chemical innovation

(2010) Anne Osbourn   TRENDS IN GENETICS

Copy Number Variation and Transposable Elements Feature in Recent, Ongoing Adaptation at the Cyp6g1 Locus

(2010) Joshua M. Schmidt et al.   PLoS Genetics

The life and death of gene families

(2009) Jeffery P. Demuth et al.   BIOESSAYS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Comparative genomic analyses of the human fungal pathogens Coccidioides and their relatives

(2009) T. J. Sharpton et al.   GENOME RESEARCH

Transformation of Phomopsis viticola with the green fluorescent protein

(2009) Daniel J. Anco et al.   MYCOLOGIA

Evolution of pathogenicity and sexual reproduction in eight Candida genomes

(2009) Geraldine Butler et al.   NATURE

Genome, transcriptome, and secretome analysis of wood decay fungusPostia placentasupports unique mechanisms of lignocellulose conversion

(2009) Diego Martinez et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Ascomycota Tree of Life: A Phylum-wide Phylogeny Clarifies the Origin and Evolution of Fundamental Reproductive and Ecological Traits

(2009) Conrad L. Schoch et al.   SYSTEMATIC BIOLOGY

Efflux in Fungi: La Pièce de Résistance

(2009) Jeffrey J. Coleman et al.   PLoS Pathogens

Living in two Worlds: The Plant and Insect Lifestyles ofXylella fastidiosa

(2008) Subhadeep Chatterjee et al.   Annual Review of Phytopathology

Altered patterns of gene duplication and differential gene gain and loss in fungal pathogens

(2008) Amy J Powell et al.   BMC GENOMICS

The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis

(2008) F. Martin et al.   NATURE

Turning a hobby into a job: How duplicated genes find new functions

(2008) Gavin C. Conant et al.   NATURE REVIEWS GENETICS

The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics

(2008) B. L. Cantarel et al.   NUCLEIC ACIDS RESEARCH

Pathogenesis ofEutypa latain Grapevine: Identification of Virulence Factors and Biochemical Characterization of Cordon Dieback

(2008) P. E. Rolshausen et al.   PHYTOPATHOLOGY