Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus

Whole genome comparative analysis of transposable elements provides new insight into mechanisms of their inactivation in fungal genomes

(2015) Joëlle Amselem et al.   BMC GENOMICS

Genomic and transcriptomic analysis of Laccaria bicolor CAZome reveals insights into polysaccharides remodelling during symbiosis establishment

(2014) Claire Veneault-Fourrey et al.   FUNGAL GENETICS AND BIOLOGY

Degeneration of the Nonrecombining Regions in the Mating-Type Chromosomes of the Anther-Smut Fungi

(2014) Eric Fontanillas et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

MITEs in the promoters of effector genes allow prediction of novel virulence genes in Fusarium oxysporum

(2013) Sarah M Schmidt et al.   BMC GENOMICS

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

(2013) Pierre Gladieux et al.   MOLECULAR ECOLOGY

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Loss and Retention of RNA Interference in Fungi and Parasites

(2013) Francisco E. Nicolás et al.   PLoS Pathogens

A normalization strategy for comparing tag count data

(2012) Koji Kadota et al.   Algorithms for Molecular Biology

LINKAGE TO THE MATING-TYPE LOCUS ACROSS THE GENUSMICROBOTRYUM: INSIGHTS INTO NONRECOMBINING CHROMOSOMES

(2012) Elsa Petit et al.   EVOLUTION

SIBLING COMPETITION ARENA: SELFING AND A COMPETITION ARENA CAN COMBINE TO CONSTITUTE A BARRIER TO GENE FLOW IN SYMPATRY

(2012) A. K. Gibson et al.   EVOLUTION

Extensive Divergence Between Mating-Type Chromosomes of the Anther-Smut Fungus

(2012) M. E. Hood et al.   GENETICS

Patterns of Repeat-Induced Point Mutation in Transposable Elements of Basidiomycete Fungi

(2012) Felix Horns et al.   Genome Biology and Evolution

Sex, outcrossing and mating types: unsolved questions in fungi and beyond

(2012) S. BILLIARD et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

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

(2012) D. Floudas et al.   SCIENCE

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Degeneration in Codon Usage within the Region of Suppressed Recombination in the Mating-Type Chromosomes of Neurospora tetrasperma

(2011) C. A. Whittle et al.   EUKARYOTIC CELL

Evidence of the accumulation of allele-specific non-synonymous substitutions in the young region of recombination suppression within the mating-type chromosomes of Neurospora tetrasperma

(2011) C A Whittle et al.   HEREDITY

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

Reorganizing the protein space at the Universal Protein Resource (UniProt)

(2011)   NUCLEIC ACIDS RESEARCH

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

S-MART, A Software Toolbox to Aid RNA-seq Data Analysis

(2011) Matthias Zytnicki et al.   PLoS One

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

About PAR: The distinct evolutionary dynamics of the pseudoautosomal region

(2011) Sarah P. Otto et al.   TRENDS IN GENETICS

Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations

(2011) Thierry Rouxel et al.   Nature Communications

Assigning duplication events to relative temporal scales in genome-wide studies

(2010) J. Huerta-Cepas et al.   BIOINFORMATICS

Having sex, yes, but with whom? Inferences from fungi on the evolution of anisogamy and mating types

(2010) Sylvain Billiard et al.   BIOLOGICAL REVIEWS

The illustrated life cycle of Microbotryum on the host plant Silene latifolia

(2010) Angela Maria Schäfer et al.   Botany

A Brief History of the Status of Transposable Elements: From Junk DNA to Major Players in Evolution

(2010) C. Biemont   GENETICS

The mutational spectrum of non-CpG DNA varies with CpG content

(2010) J.-C. Walser et al.   GENOME RESEARCH

Comprehensive comparative analysis of strand-specific RNA sequencing methods

(2010) Joshua Z Levin et al.   NATURE METHODS

PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions

(2010) J. Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Ongoing and future developments at the Universal Protein Resource

(2010)   NUCLEIC ACIDS RESEARCH

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

(2010) A. Zemach et al.   SCIENCE

A Novel High-Affinity Sucrose Transporter Is Required for Virulence of the Plant Pathogen Ustilago maydis

(2010) Ramon Wahl et al.   PLOS BIOLOGY

Polyamines: ubiquitous polycations with unique roles in growth and stress responses

(2009) Taku Takahashi et al.   ANNALS OF BOTANY

Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes

(2009) Laurent Duret et al.   Annual Review of Genomics and Human Genetics

Fungal Effector Proteins

(2009) Ioannis Stergiopoulos et al.   Annual Review of Phytopathology

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

A White Campion (Silene latifolia) floral expressed sequence tag (EST) library: annotation, EST-SSR characterization, transferability, and utility for comparative mapping

(2009) Maria Moccia et al.   BMC GENOMICS

Evolutionary Strata in a Small Mating-Type-Specific Region of the Smut Fungus Microbotryum violaceum

(2009) Antonina A Votintseva et al.   GENETICS

Hybrid sterility and inviability in the parasitic fungal species complexMicrobotryum

(2009) D. M. DE VIENNE et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Phylogenetic determinants of potential host shifts in fungal pathogens

(2009) D. M. de VIENNE et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Can GC Content at Third-Codon Positions Be Used as a Proxy for Isochore Composition?

(2009) E. Elhaik et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans

(2009) Brian J. Haas et al.   NATURE

PROSITE, a protein domain database for functional characterization and annotation

(2009) Christian J. A. Sigrist et al.   NUCLEIC ACIDS RESEARCH

Transcriptome analysis by strand-specific sequencing of complementary DNA

(2009) Dmitri Parkhomchuk et al.   NUCLEIC ACIDS RESEARCH

Hidden diversity in the non‐caryophyllaceous plant‐parasitic members ofMicrobotryum(Pucciniomycotina: Microbotryales)

(2009) Martin Kemler et al.   SYSTEMATICS AND BIODIVERSITY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

RIPCAL: a tool for alignment-based analysis of repeat-induced point mutations in fungal genomic sequences

(2008) James K Hane et al.   BMC BIOINFORMATICS

PredGPI: a GPI-anchor predictor

(2008) Andrea Pierleoni et al.   BMC BIOINFORMATICS

Cophylogeny of the anther smut fungi and their caryophyllaceous hosts: Prevalence of host shifts and importance of delimiting parasite species for inferring cospeciation

(2008) Guislaine Refrégier et al.   BMC EVOLUTIONARY BIOLOGY

Mating System of the Anther Smut FungusMicrobotryum violaceum: Selfing under Heterothallism

(2008) Tatiana Giraud et al.   EUKARYOTIC CELL

Ancient Trans-specific Polymorphism at Pheromone Receptor Genes in Basidiomycetes

(2008) B. Devier et al.   GENETICS

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

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

The Mating-Type Chromosome in the Filamentous Ascomycete Neurospora tetrasperma Represents a Model for Early Evolution of Sex Chromosomes

(2008) Audrius Menkis et al.   PLoS Genetics

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY