Comparative genomics and prediction of conditionally dispensable sequences in legume–infecting Fusarium oxysporum formae speciales facilitates identification of candidate effectors

Comparative genomics of Fusarium oxysporum f. sp. melonis reveals the secreted protein recognized by the Fom-2 resistance gene in melon

(2015) Sarah Maria Schmidt et al.   NEW PHYTOLOGIST

TheAVR2-SIX5gene pair is required to activateI-2-mediated immunity in tomato

(2015) Lisong Ma et al.   NEW PHYTOLOGIST

Fusarium oxysporumf. sp.canariensis: evidence for horizontal gene transfer of putative pathogenicity genes

(2015) M. H. Laurence et al.   PLANT PATHOLOGY

Putative effector genes detected inFusarium oxysporumfrom natural ecosystems of Australia

(2015) L. O. Rocha et al.   PLANT PATHOLOGY

UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches

(2014) B. E. Suzek et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Analysis of root proteome unravels differential molecular responses during compatible and incompatible interaction between chickpea (Cicer arietinum L.) and Fusarium oxysporum f. sp. ciceri Race1 (Foc1)

(2014) Moniya Chatterjee et al.   BMC GENOMICS

Introduction: Legumes in Sustainable Agriculture

(2014) Diego Rubiales et al.   CRITICAL REVIEWS IN PLANT SCIENCES

Achievements and Challenges in Legume Breeding for Pest and Disease Resistance

(2014) Diego Rubiales et al.   CRITICAL REVIEWS IN PLANT SCIENCES

Multilocus Analysis Using Putative Fungal Effectors to Describe a Population ofFusarium oxysporumfrom Sugar Beet

(2014) Paul A. Covey et al.   PHYTOPATHOLOGY

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

(2013) Sarah M Schmidt et al.   BMC GENOMICS

The Fusarium oxysporum Effector Six6 Contributes to Virulence and Suppresses I-2-Mediated Cell Death

(2013) F. Gawehns et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Evolution, selection and isolation: a genomic view of speciation in fungal plant pathogens

(2013) Eva Holtgrewe Stukenbrock   NEW PHYTOLOGIST

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

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

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Sequence variation in the putative effector geneSIX8facilitates molecular differentiation ofFusarium oxysporumf. sp.cubense

(2013) S. Fraser-Smith et al.   PLANT PATHOLOGY

Deciphering the Cryptic Genome: Genome-wide Analyses of the Rice Pathogen Fusarium fujikuroi Reveal Complex Regulation of Secondary Metabolism and Novel Metabolites

(2013) Philipp Wiemann et al.   PLoS Pathogens

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Presence of putative pathogenicity genes in isolates of Fusarium oxysporum f. sp. cubense from Australia

(2012) R. A. Meldrum et al.   AUSTRALASIAN PLANT PATHOLOGY

Origin of pisatin demethylase (PDA) in the genus Fusarium

(2012) Nicholas A. Milani et al.   FUNGAL GENETICS AND BIOLOGY

The Top 10 fungal pathogens in molecular plant pathology

(2012) RALPH DEAN et al.   MOLECULAR PLANT PATHOLOGY

Genomic tillage and the harvest of fungal phytopathogens

(2012) Richard Oliver   NEW PHYTOLOGIST

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

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

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

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

Development of genomic resources for the narrow-leafed lupin (Lupinus angustifolius): construction of a bacterial artificial chromosome (BAC) library and BAC-end sequencing

(2011) Ling-Ling Gao et al.   BMC GENOMICS

Current status of the taxonomic position of Fusarium oxysporum formae specialis cubense within the Fusarium oxysporum complex

(2011) G. Fourie et al.   INFECTION GENETICS AND EVOLUTION

Characterization of the Gene Encoding Pisatin Demethylase (FoPDA1) inFusarium oxysporum

(2011) Jeffrey J. Coleman et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

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

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

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Thierry Rouxel et al.   Nature Communications

Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis

(2011) Stephen B. Goodwin et al.   PLoS Genetics

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

ETE: a python Environment for Tree Exploration

(2010) Jaime Huerta-Cepas et al.   BMC BIOINFORMATICS

Hidden Markov model speed heuristic and iterative HMM search procedure

(2010) L Steven Johnson et al.   BMC BIOINFORMATICS

Effector proteins of extracellular fungal plant pathogens that trigger host resistance

(2010) Ann-Maree Catanzariti et al.   FUNCTIONAL PLANT BIOLOGY

SMURF: Genomic mapping of fungal secondary metabolite clusters

(2010) Nora Khaldi et al.   FUNGAL GENETICS AND BIOLOGY

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

(2010) Li-Jun Ma et al.   NATURE

Variation in potential effector genes distinguishing Australian and non-Australian isolates of the cotton wilt pathogen Fusarium oxysporum f.sp. vasinfectum

(2010) A. Chakrabarti et al.   PLANT PATHOLOGY

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fungal Effector Proteins

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

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

A study on the susceptibility of the model legume plant Medicago truncatula to the soil-borne pathogen Fusarium oxysporum

(2009) Montserrat Ramírez-Suero et al.   EUROPEAN JOURNAL OF PLANT PATHOLOGY

Effector gene screening allows unambiguous identification ofFusarium oxysporumf. sp.lycopersici races and discrimination from otherformae speciales

(2009) Bart Lievens et al.   FEMS MICROBIOLOGY LETTERS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Fungal effector proteins: past, present and future

(2009) PIERRE J. G. M. DE WIT et al.   MOLECULAR PLANT PATHOLOGY

Pathogen profile update:Fusarium oxysporum

(2009) CAROLINE B. MICHIELSE et al.   MOLECULAR PLANT PATHOLOGY

Microbiological control of soil-borne phytopathogenic fungi with special emphasis on wilt-inducingFusarium oxysporum

(2009) Claude Alabouvette et al.   NEW PHYTOLOGIST

The effector protein Avr2 of the xylem-colonizing fungusFusarium oxysporumactivates the tomato resistance protein I-2 intracellularly

(2009) Petra M. Houterman et al.   PLANT JOURNAL

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

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

Gene prediction in novel fungal genomes using an ab initio algorithm with unsupervised training

(2008) V. Ter-Hovhannisyan et al.   GENOME RESEARCH

The novelCladosporium fulvumlysin motif effector Ecp6 is a virulence factor with orthologues in other fungal species

(2008) Melvin D. Bolton et al.   MOLECULAR MICROBIOLOGY

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

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

Rfam: updates to the RNA families database

(2008) P. P. Gardner et al.   NUCLEIC ACIDS RESEARCH

Recent developments in the molecular discrimination offormae specialesofFusarium oxysporum

(2008) Bart Lievens et al.   PEST MANAGEMENT SCIENCE

Alternaria brassicaeProduces a Host-Specific Protein Toxin from Germinating Spores on Host Leaves

(2008) R. Y. Parada et al.   PHYTOPATHOLOGY

Suppression of Plant Resistance Gene-Based Immunity by a Fungal Effector

(2008) Petra M. Houterman et al.   PLoS Pathogens

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

(2008) Brian J Haas et al.   GENOME BIOLOGY