Characterisation of pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp. cepae

Races of the Celery Pathogen Fusarium oxysporum f. sp. apii Are Polyphyletic

(2017) Lynn Epstein et al.   PHYTOPATHOLOGY

Multiple Evolutionary Trajectories Have Led to the Emergence of Races in Fusarium oxysporum f. sp. lycopersici

(2016) V. Chellappan Biju et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Exchange of core chromosomes and horizontal transfer of lineage-specific chromosomes in Fusarium oxysporum

(2016) Ido Vlaardingerbroek et al.   ENVIRONMENTAL MICROBIOLOGY

Effector profiles distinguish formae speciales of Fusarium oxysporum

(2016) Peter van Dam et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2016) Luigi Faino et al.   GENOME RESEARCH

TheFTFgene family regulates virulence and expression of SIX effectors inFusarium oxysporum

(2016) Jonathan Niño-Sánchez et al.   MOLECULAR PLANT PATHOLOGY

Identification of pathogenicity-related genes inFusarium oxysporumf. sp.cepae

(2016) Andrew Taylor et al.   MOLECULAR PLANT PATHOLOGY

Transcription Factors Encoded on Core and Accessory Chromosomes of Fusarium oxysporum Induce Expression of Effector Genes

(2016) H. Charlotte van der Does et al.   PLoS Genetics

Non-canonical Helitrons in Fusarium oxysporum

(2016) Biju Vadakkemukadiyil Chellapan et al.   Mobile DNA

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS: Table 1.

(2015) Katharina J. Hoff et al.   BIOINFORMATICS

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

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

(2015) Alison C Testa et al.   BMC GENOMICS

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

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

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

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

(2015) Jana Sperschneider et al.   NEW PHYTOLOGIST

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

(2015) Lisong Ma et al.   NEW PHYTOLOGIST

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

Genetic and Pathogenic Variability of Fusarium oxysporum f. sp. cepae Isolated from Onion and Welsh Onion in Japan

(2015) Kazunori Sasaki et al.   PHYTOPATHOLOGY

The effector repertoire of Fusarium oxysporum determines the tomato xylem proteome composition following infection

(2015) Fleur Gawehns et al.   Frontiers in Plant Science

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Effectors as Tools in Disease Resistance Breeding Against Biotrophic, Hemibiotrophic, and Necrotrophic Plant Pathogens

(2014) Vivianne G. A. A. Vleeshouwers et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

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

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

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Endophytic Strain Fusarium oxysporum Fo47: A Good Candidate for Priming the Defense Responses in Tomato Roots

(2013) Sébastien Aimé et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

The carbohydrate-active enzymes database (CAZy) in 2013

(2013) Vincent Lombard et al.   NUCLEIC ACIDS RESEARCH

Comparative Genomic and Transcriptomic Analysis of Tandemly and Segmentally Duplicated Genes in Rice

(2013) Shu-Ye Jiang et al.   PLoS One

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

(2012) R. Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Phylogenetic and Biological Characterization ofFusarium oxysporumIsolates Associated with Onion in South Africa

(2012) Michael J. Southwood et al.   PLANT DISEASE

Identification of differential resistance to sixFusarium oxysporumf. sp.cepaeisolates in commercial onion cultivars through the development of a rapid seedling assay

(2012) A. Taylor et al.   PLANT PATHOLOGY

Rate variation and estimation of divergence times using strict and relaxed clocks

(2011) Richard P Brown et al.   BMC EVOLUTIONARY BIOLOGY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Molecular Identification of Two Vegetative Compatibility Groups ofFusarium oxysporumf. sp.cepae

(2011) Michael J. Southwood et al.   PHYTOPATHOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Molecular Identification and Genetic Diversity of Fusarium species Associated with Onion Fields in Turkey

(2010) Harun Bayraktar et al.   JOURNAL OF PHYTOPATHOLOGY

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

(2010) Li-Jun Ma et al.   NATURE

Genetic linkage and natural selection

(2010) N. H. Barton   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The Nuclear Protein Sge1 of Fusarium oxysporum Is Required for Parasitic Growth

(2009) Caroline B. Michielse et al.   PLoS Pathogens

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

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