The Complete Genome Sequence of the Phytopathogenic Fungus Sclerotinia sclerotiorum Reveals Insights into the Genome Architecture of Broad Host Range Pathogens

Mind the gap; seven reasons to close fragmented genome assemblies

(2016) Bart P.H.J. Thomma et al.   FUNGAL GENETICS AND BIOLOGY

Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen

(2016) Luigi Faino et al.   GENOME RESEARCH

A gapless genome sequence of the fungusBotrytis cinerea

(2016) Jan A. L. Van Kan et al.   MOLECULAR PLANT PATHOLOGY

A Fungal Effector With Host Nuclear Localization and DNA-Binding Properties Is Required for Maize Anthracnose Development

(2016) Walter A. Vargas et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Phytophthora infestans Argonaute 1 binds microRNA and small RNAs from effector genes and transposable elements

(2016) Anna K. M. Åsman et al.   NEW PHYTOLOGIST

Comprehensive Annotation of the Parastagonospora nodorum Reference Genome Using Next-Generation Genomics, Transcriptomics and Proteogenomics

(2016) Robert A. Syme et al.   PLoS One

A Small Secreted Virulence-Related Protein Is Essential for the Necrotrophic Interactions of Sclerotinia sclerotiorum with Its Host Plants

(2016) Xueliang Lyu et al.   PLoS Pathogens

Fungal Effectors and Plant Susceptibility

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

CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts

(2015) Alison C Testa et al.   BMC GENOMICS

Evolution of the EKA family of powdery mildew avirulence-effector genes from the ORF 1 of a LINE retrotransposon

(2015) Joelle Amselem et al.   BMC GENOMICS

The completed genome sequence of the pathogenic ascomycete fungus Fusarium graminearum

(2015) Robert King et al.   BMC GENOMICS

The two-speed genomes of filamentous pathogens: waltz with plants

(2015) Suomeng Dong et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

A ToxA-like protein from Cochliobolus heterostrophus induces light-dependent leaf necrosis and acts as a virulence factor with host selectivity on maize

(2015) Shunwen Lu et al.   FUNGAL GENETICS AND BIOLOGY

Broadly Conserved Fungal Effector BEC1019 Suppresses Host Cell Death and Enhances Pathogen Virulence in Powdery Mildew of Barley (Hordeum vulgare L.) (Retracted)

(2015) Ehren Whigham et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

The fungal core effector Pep1 is conserved across smuts of dicots and monocots

(2015) Christoph Hemetsberger et al.   NEW PHYTOLOGIST

Effector P: predicting fungal effector proteins from secretomes using machine learning

(2015) Jana Sperschneider et al.   NEW PHYTOLOGIST

PhytoPath: an integrative resource for plant pathogen genomics

(2015) Helder Pedro et al.   NUCLEIC ACIDS RESEARCH

Transcriptome and Metabolite Profiling of the Infection Cycle ofZymoseptoria triticion Wheat Reveals a Biphasic Interaction with Plant Immunity Involving Differential Pathogen Chromosomal Contributions and a Variation on the Hemibiotrophic Lifestyle Definition

(2015) Jason J. Rudd et al.   PLANT PHYSIOLOGY

Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome

(2015) Luigi Faino et al.   mBio

Advances and Challenges in Computational Prediction of Effectors from Plant Pathogenic Fungi

(2015) Jana Sperschneider et al.   PLoS Pathogens

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Secretome analysis reveals effector candidates associated with broad host range necrotrophy in the fungal plant pathogen Sclerotinia sclerotiorum

(2014) Koanna Guyon et al.   BMC GENOMICS

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

(2014) Jonathan Grandaubert et al.   BMC GENOMICS

Analysis of Tc1-Mariner elements in Sclerotinia sclerotiorum suggests recent activity and flexible transposases

(2014) Mateus F Santana et al.   BMC MICROBIOLOGY

A field guide to whole-genome sequencing, assembly and annotation

(2014) Robert Ekblom et al.   Evolutionary Applications

Oxaloacetate acetylhydrolase gene mutants ofSclerotinia sclerotiorumdo not accumulate oxalic acid, but do produce limited lesions on host plants

(2014) Xiaofei Liang et al.   MOLECULAR PLANT PATHOLOGY

A novel protein elicitor (SsCut) from Sclerotinia sclerotiorum induces multiple defense responses in plants

(2014) Huajian Zhang et al.   PLANT MOLECULAR BIOLOGY

Early allopolyploid evolution in the post-Neolithic Brassica napus oilseed genome

(2014) B. Chalhoub et al.   SCIENCE

The role of effectors and host immunity in plant–necrotrophic fungal interactions

(2014) Xuli Wang et al.   Virulence

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

A Secretory Protein of Necrotrophic Fungus Sclerotinia sclerotiorum That Suppresses Host Resistance

(2013) Wenjun Zhu et al.   PLoS One

Structure and evolution of barley powdery mildew effector candidates

(2012) Carsten Pedersen et al.   BMC GENOMICS

Disruption of a gene encoding a hypothetical secreted protein fromSclerotinia sclerotiorumreduces its virulence on canola (Brassica napus)

(2012) Yue Liang et al.   CANADIAN JOURNAL OF PLANT PATHOLOGY

Centromeres of filamentous fungi

(2012) Kristina M. Smith et al.   CHROMOSOME RESEARCH

TheBotrytis cinereacerato-platanin BcSpl1 is a potent inducer of systemic acquired resistance (SAR) in tobacco and generates a wave of salicylic acid expanding from the site of application

(2012) Marcos Frías et al.   MOLECULAR PLANT PATHOLOGY

The Top 10 fungal pathogens in molecular plant pathology

(2012) RALPH DEAN et al.   MOLECULAR PLANT PATHOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Dfam: a database of repetitive DNA based on profile hidden Markov models

(2012) Travis J. Wheeler et al.   NUCLEIC ACIDS RESEARCH

Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology

(2012) Adam C. English et al.   PLoS One

Defining the Predicted Protein Secretome of the Fungal Wheat Leaf Pathogen Mycosphaerella graminicola

(2012) Alexandre Morais do Amaral et al.   PLoS One

Sequential Delivery of Host-Induced Virulence Effectors by Appressoria and Intracellular Hyphae of the Phytopathogen Colletotrichum higginsianum

(2012) Jochen Kleemann et al.   PLoS Pathogens

The Accessory Genome as a Cradle for Adaptive Evolution in Pathogens

(2012) Daniel Croll 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

A Highly Conserved Effector in Fusarium oxysporum Is Required for Full Virulence on Arabidopsis

(2011) Louise F. Thatcher et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Metabolic priming by a secreted fungal effector

(2011) Armin Djamei et al.   NATURE

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

BcSpl1, a cerato-platanin family protein, contributes to Botrytis cinerea virulence and elicits the hypersensitive response in the host

(2011) Marcos Frías et al.   NEW PHYTOLOGIST

Analysis of Two in Planta Expressed LysM Effector Homologs from the Fungus Mycosphaerella graminicola Reveals Novel Functional Properties and Varying Contributions to Virulence on Wheat

(2011) R. Marshall et al.   PLANT PHYSIOLOGY

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

(2011) Thierry Rouxel et al.   Nature Communications

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

(2011) Joelle Amselem et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

(2010) Li-Jun Ma et al.   NATURE

Host-selective toxins, Ptr ToxA and Ptr ToxB, as necrotrophic effectors in the Pyrenophora tritici-repentis-wheat interaction

(2010) Lynda M. Ciuffetti et al.   NEW PHYTOLOGIST

Genome Evolution Following Host Jumps in the Irish Potato Famine Pathogen Lineage

(2010) S. Raffaele et al.   SCIENCE

Conserved Fungal LysM Effector Ecp6 Prevents Chitin-Triggered Immunity in Plants

(2010) R. de Jonge et al.   SCIENCE

Fungal Effector Proteins

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

Characterization of a canola C2 domain gene that interacts with PG, an effector of the necrotrophic fungus Sclerotinia sclerotiorum

(2009) X. Wang et al.   JOURNAL OF EXPERIMENTAL BOTANY

Expression and regulation ofSclerotinia sclerotiorumnecrosis and ethylene-inducing peptides (NEPs)

(2009) ZAFER DALLAL BASHI et al.   MOLECULAR PLANT PATHOLOGY

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

(2009) Brian J. Haas et al.   NATURE

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

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Host-specific toxins: effectors of necrotrophic pathogenicity

(2008) Timothy L. Friesen et al.   CELLULAR MICROBIOLOGY

Biocontrol of Lettuce Drop Caused bySclerotinia sclerotiorumandS. minorin Desert Agroecosystems

(2008) P. Chitrampalam et al.   PLANT DISEASE

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

(2008) Brian J Haas et al.   GENOME BIOLOGY