Comparative Genomics of Pathogenic and Nonpathogenic Beetle-Vectored Fungi in the Genus Geosmithia

OcculterCut: A Comprehensive Survey of AT-Rich Regions in Fungal Genomes

(2016) Alison C. Testa et al.   Genome Biology and Evolution

Small genome of the fungusEscovopsis weberi, a specialized disease agent of ant agriculture

(2016) Tom J. B. de Man et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A novel transcription factor gene FHS1 is involved in the DNA damage response in Fusarium graminearum

(2016) Hokyoung Son et al.   Scientific Reports

De novogenome assembly ofGeosmithia morbida, the causal agent of thousand cankers disease

(2016) Taruna A. Schuelke et al.   PeerJ

Fungal Effectors and Plant Susceptibility

(2015) Libera Lo Presti et al.   Annual Review of Plant Biology

BFC: correcting Illumina sequencing errors

(2015) Heng Li   BIOINFORMATICS

Insights on the Evolution of Mycoparasitism from the Genome of Clonostachys rosea

(2015) Magnus Karlsson et al.   Genome Biology and Evolution

Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists

(2015) Annegret Kohler et al.   NATURE GENETICS

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

(2015) Tilmann Weber et al.   NUCLEIC ACIDS RESEARCH

Ensembl Genomes 2016: more genomes, more complexity

(2015) Paul Julian Kersey et al.   NUCLEIC ACIDS RESEARCH

Twenty years of theMEROPSdatabase of proteolytic enzymes, their substrates and inhibitors

(2015) Neil D. Rawlings et al.   NUCLEIC ACIDS RESEARCH

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Selecting optimal partitioning schemes for phylogenomic datasets

(2014) Robert Lanfear et al.   BMC EVOLUTIONARY BIOLOGY

Functional Annotation of the Ophiostoma novo-ulmi Genome: Insights into the Phytopathogenicity of the Fungal Agent of Dutch Elm Disease

(2014) André M. Comeau et al.   Genome Biology and Evolution

Novel Information Theory-Based Measures for Quantifying Incongruence among Phylogenetic Trees

(2014) Leonidas Salichos et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparative Genomics of the Pine Pathogens and Beetle Symbionts in the Genus Grosmannia

(2014) Sepideh Massoumi Alamouti et al.   MOLECULAR BIOLOGY AND EVOLUTION

First Report of Geosmithia pallida Causing Foamy Bark Canker, a New Disease on Coast Live Oak (Quercus agrifolia), in Association with Pseudopityophthorus pubipennis in California

(2014) S. C. Lynch et al.   PLANT DISEASE

Population Structure of Geosmithia morbida, the Causal Agent of Thousand Cankers Disease of Walnut Trees in the United States

(2014) Marcelo M. Zerillo et al.   PLoS One

The evolving fungal genome

(2014) Eva H. Stukenbrock et al.   Fungal Biology Reviews

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Selecting informative subsets of sparse supermatrices increases the chance to find correct trees

(2013) Bernhard Misof et al.   BMC BIOINFORMATICS

Sequencing and annotation of the Ophiostoma ulmi genome

(2013) Shima Khoshraftar et al.   BMC GENOMICS

Vector Affinity and Diversity of Geosmithia Fungi Living on Subcortical Insects Inhabiting Pinaceae Species in Central and Northeastern Europe

(2013) Miroslav Kolařík et al.   MICROBIAL ECOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The impact of transposable elements in environmental adaptation

(2013) Elena Casacuberta et al.   MOLECULAR ECOLOGY

Destructive Tree Diseases Associated with Ambrosia and Bark Beetles: Black Swan Events in Tree Pathology?

(2013) Randy C. Ploetz et al.   PLANT DISEASE

Comparative Genomics Reveals Insight into Virulence Strategies of Plant Pathogenic Oomycetes

(2013) Bishwo N. Adhikari et al.   PLoS One

Cell Death Control: The Interplay of Apoptosis and Autophagy in the Pathogenicity of Sclerotinia sclerotiorum

(2013) Mehdi Kabbage et al.   PLoS Pathogens

Fungal laccase, manganese peroxidase and lignin peroxidase: Gene expression and regulation

(2012) Grzegorz Janusz et al.   ENZYME AND MICROBIAL TECHNOLOGY

Genome Update of Botrytis cinerea Strains B05.10 and T4

(2012) Martijn Staats et al.   EUKARYOTIC CELL

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

Susceptibility of Walnut and Hickory Species to Geosmithia morbida

(2012) Curtis Utley et al.   PLANT DISEASE

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Geosmithia morbida sp. nov., a new phytopathogenic species living in symbiosis with the walnut twig beetle (Pityophthorus juglandis) on Juglans in USA

(2011) Miroslav Kolařík et al.   MYCOLOGIA

Modulation of ethanol stress tolerance by aldehyde dehydrogenase in the mycorrhizal fungus Tricholoma vaccinum

(2011) Theodore Asiimwe et al.   MYCORRHIZA

Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestris

(2011) Randy M Berka et al.   NATURE BIOTECHNOLOGY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

MACSE: Multiple Alignment of Coding SEquences Accounting for Frameshifts and Stop Codons

(2011) Vincent Ranwez et al.   PLoS One

Genome and transcriptome analyses of the mountain pine beetle-fungal symbiont Grosmannia clavigera, a lodgepole pine pathogen

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

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

(2011) Joelle Amselem et al.   PLoS Genetics

The bZIP Transcription Factor MoAP1 Mediates the Oxidative Stress Response and Is Critical for Pathogenicity of the Rice Blast Fungus Magnaporthe oryzae

(2011) Min Guo et al.   PLoS Pathogens

Genome sequence of the insect pathogenic fungus Cordyceps militaris, a valued traditional chinese medicine

(2011) Peng Zheng et al.   GENOME BIOLOGY

Comparative genome sequence analysis underscores mycoparasitism as the ancestral life style of Trichoderma

(2011) Christian P Kubicek et al.   GENOME BIOLOGY

Evidence for a new lineage of primary ambrosia fungi in Geosmithia Pitt (Ascomycota: Hypocreales)

(2010) Miroslav Kolařík et al.   Fungal Biology

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

(2010) Li-Jun Ma et al.   NATURE

Genome Expansion and Gene Loss in Powdery Mildew Fungi Reveal Tradeoffs in Extreme Parasitism

(2010) P. D. Spanu et al.   SCIENCE

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

A fungal phylogeny based on 82 complete genomes using the composition vector method

(2009) Hao Wang et al.   BMC EVOLUTIONARY BIOLOGY

Reduced genomic potential for secreted plant cell-wall-degrading enzymes in the ectomycorrhizal fungus Amanita bisporigera, based on the secretome of Trichoderma reesei

(2009) Subashini Nagendran et al.   FUNGAL GENETICS AND BIOLOGY

ABySS: A parallel assembler for short read sequence data

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

Innate Immunity in Plants: An Arms Race Between Pattern Recognition Receptors in Plants and Effectors in Microbial Pathogens

(2009) T. Boller et al.   SCIENCE

A Putative ABC Transporter Confers Durable Resistance to Multiple Fungal Pathogens in Wheat

(2009) S. G. Krattinger et al.   SCIENCE

The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion

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

Secondary metabolism: regulation and role in fungal biology

(2008) Ellen M Fox et al.   CURRENT OPINION IN MICROBIOLOGY

Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina)

(2008) Diego Martinez et al.   NATURE BIOTECHNOLOGY

The Role of bZIP Transcription Factors in Green Plant Evolution: Adaptive Features Emerging from Four Founder Genes

(2008) Luiz Gustavo Guedes Corrêa et al.   PLoS One