Transposable element-assisted evolution and adaptation to host plant within the Leptosphaeria maculans-Leptosphaeria biglobosa species complex of fungal pathogens

Epigenetic Control of Effector Gene Expression in the Plant Pathogenic Fungus Leptosphaeria maculans

(2014) Jessica L. Soyer et al.   PLoS Genetics

The wheat powdery mildew genome shows the unique evolution of an obligate biotroph

(2013) Thomas Wicker et al.   NATURE GENETICS

The dispensable chromosome ofLeptosphaeria maculansshelters an effector gene conferring avirulence towardsBrassica rapa

(2013) Marie-Hélène Balesdent et al.   NEW PHYTOLOGIST

Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis , Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence

(2013) Viola A. Manning et al.   G3-Genes Genomes Genetics

Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

(2013) Bradford J. Condon et al.   PLoS Genetics

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Migration patterns and changes in population biology associated with the worldwide spread of the oilseed rape pathogenLeptosphaeria maculans

(2012) A. DILMAGHANI et al.   MOLECULAR ECOLOGY

Attack of the Clones

(2012) K. Kupferschmidt   SCIENCE

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

(2012) D. Floudas et al.   SCIENCE

The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry

(2012) Pierre J. G. M. de Wit et al.   PLoS Genetics

Genome Structure and Reproductive Behaviour Influence the Evolutionary Potential of a Fungal Phytopathogen

(2012) Guillaume Daverdin et al.   PLoS Pathogens

Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi

(2012) Robin A. Ohm et al.   PLoS Pathogens

Rock-inhabiting fungi originated during periods of dry climate in the late Devonian and middle Triassic

(2011) Cécile Gueidan et al.   Fungal Biology

InterPro in 2011: new developments in the family and domain prediction database

(2011) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

Zymoseptoria gen. nov.: a new genus to accommodate Septoria-like species occurring on graminicolous hosts

(2011) W. Quaedvlieg et al.   PERSOONIA

Transcriptional Programming and Functional Interactions within thePhytophthora sojaeRXLR Effector Repertoire

(2011) Qunqing Wang et al.   PLANT CELL

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre 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

Multiple Translocation of the AVR-Pita Effector Gene among Chromosomes of the Rice Blast Fungus Magnaporthe oryzae and Related Species

(2011) Izumi Chuma et al.   PLoS Pathogens

A novel mode of chromosomal evolution peculiar to filamentous Ascomycete fungi

(2011) James K Hane et al.   GENOME BIOLOGY

ANAIS: Analysis of NimbleGen Arrays Interface

(2010) A. Simon et al.   BIOINFORMATICS

In silico reversal of repeat-induced point mutation (RIP) identifies the origins of repeat families and uncovers obscured duplicated genes

(2010) James K Hane et al.   BMC GENOMICS

Genomic evidence of repeat-induced point mutation (RIP) in filamentous ascomycetes

(2010) A. John Clutterbuck   FUNGAL GENETICS AND BIOLOGY

Jumping genes and epigenetics: Towards new species

(2010) Rita Rebollo et al.   GENE

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Dated molecular phylogenies indicate a Miocene origin for Arabidopsis thaliana

(2010) M. A. Beilstein et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) P. D. Spanu et al.   SCIENCE

Evolution of Linked Avirulence Effectors in Leptosphaeria maculans Is Affected by Genomic Environment and Exposure to Resistance Genes in Host Plants

(2010) Angela P. Van de Wouw et al.   PLoS Pathogens

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

Recovering genome rearrangements in the mammalian phylogeny

(2009) H. Zhao et al.   GENOME RESEARCH

Repeat-Induced Point Mutation (RIP) as an Alternative Mechanism of Evolution Toward Virulence inLeptosphaeria maculans

(2009) Isabelle Fudal et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Unravelling Mycosphaerella: do you believe in genera?

(2009) P.W. Crous et al.   PERSOONIA

The Transposon Galileo Generates Natural Chromosomal Inversions in Drosophila by Ectopic Recombination

(2009) Alejandra Delprat et al.   PLoS One

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

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

(2008) James K Hane et al.   BMC BIOINFORMATICS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Revisiting horizontal transfer of transposable elements in Drosophila

(2008) E L S Loreto et al.   HEREDITY

Leptosphaeria maculansavirulence geneAvrLm4-7confers a dual recognition specificity by theRlm4andRlm7resistance genes of oilseed rape, and circumventsRlm4-mediated recognition through a single amino acid change

(2008) Francis Parlange et al.   MOLECULAR MICROBIOLOGY

A universal classification of eukaryotic transposable elements implemented in Repbase

(2008) Vladimir V. Kapitonov et al.   NATURE REVIEWS GENETICS

Occurrence of a New Subclade ofLeptosphaeria biglobosain Western Australia

(2008) L. Vincenot et al.   PHYTOPATHOLOGY

Evidence for horizontal transfer of a secondary metabolite gene cluster between fungi

(2008) Nora Khaldi et al.   GENOME BIOLOGY