Characterization of Growth Morphology and Pathology, and Draft Genome Sequencing of Botrytis fabae, the Causal Organism of Chocolate Spot of Faba Bean (Vicia faba L.)

Identification and characterization of Botrytis medusae , a novel cryptic species causing grey mould on wine grapes in Australia

(2019) L. A. Harper et al.   PLANT PATHOLOGY

Botcinic acid biosynthesis in Botrytis cinerea relies on a subtelomeric gene cluster surrounded by relics of transposons and is regulated by the Zn2Cys6 transcription factor BcBoa13

(2019) Antoine Porquier et al.   CURRENT GENETICS

Comparative genomics of plant pathogenic Botrytis species with distinct host specificity

(2019) Claudio A. Valero-Jiménez et al.   BMC GENOMICS

antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

(2019) Kai Blin et al.   NUCLEIC ACIDS RESEARCH

A transposable element annotation pipeline and expression analysis reveal potentially active elements in the microalga Tisochrysis lutea

(2018) Jérémy Berthelier et al.   BMC GENOMICS

Bioinformatic prediction of plant–pathogenicity effector proteins of fungi

(2018) Darcy AB Jones et al.   CURRENT OPINION IN MICROBIOLOGY

Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0

(2018) Jana Sperschneider et al.   MOLECULAR PLANT PATHOLOGY

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

(2018) Han Zhang et al.   NUCLEIC ACIDS RESEARCH

Many Shades of Grey in Botrytis –Host Plant Interactions

(2018) Javier Veloso et al.   TRENDS IN PLANT SCIENCE

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

(2017) Mark Derbyshire et al.   Genome Biology and Evolution

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Genome Biology of Effector Gene Evolution in Filamentous Plant Pathogens

(2016) Andrea Sánchez-Vallet et al.   Annual Review of Phytopathology

New faba bean germplasm with multiple resistances to Ascochyta blight, chocolate spot and rust diseases

(2016) Fouad Maalouf et al.   EUPHYTICA

The botrydial biosynthetic gene cluster of Botrytis cinerea displays a bipartite genomic structure and is positively regulated by the putative Zn(II)2Cys6 transcription factor BcBot6

(2016) Antoine Porquier et al.   FUNGAL GENETICS AND BIOLOGY

OcculterCut: A Comprehensive Survey of AT-Rich Regions in Fungal Genomes

(2016) Alison C. Testa et al.   Genome Biology and Evolution

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

Temporal and Spatial Development of Cercospora Leaf Spot of Faba Bean Influenced by In Situ Inoculum

(2016) R. B. E. Kimber et al.   PLANT DISEASE

Computational Prediction of Effector Proteins in Fungi: Opportunities and Challenges

(2016) Humira Sonah et al.   Frontiers in Plant Science

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

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

(2015) Jana Sperschneider et al.   NEW PHYTOLOGIST

Pathogenic attributes of Sclerotinia sclerotiorum : Switching from a biotrophic to necrotrophic lifestyle

(2015) Mehdi Kabbage et al.   PLANT SCIENCE

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

PASTEC: An Automatic Transposable Element Classification Tool

(2014) Claire Hoede et al.   PLoS One

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

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

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

Genome evolution in filamentous plant pathogens: why bigger can be better

(2012) Sylvain Raffaele et al.   NATURE REVIEWS MICROBIOLOGY

A high throughput DNA extraction method with high yield and quality

(2012) Zhanguo Xin et al.   Plant Methods

Evidence for a Common Toolbox Based on Necrotrophy in a Fungal Lineage Spanning Necrotrophs, Biotrophs, Endophytes, Host Generalists and Specialists

(2012) Marion Andrew et al.   PLoS One

Transcriptome Sequencing and Annotation for the Jamaican Fruit Bat (Artibeus jamaicensis)

(2012) Timothy I. Shaw et al.   PLoS One

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

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

Lack of evidence for a role of hydrophobins in conferring surface hydrophobicity to conidia and hyphae of Botrytis cinerea

(2011) Andreas Mosbach et al.   BMC MICROBIOLOGY

Screening faba bean for chocolate spot resistance: evaluation methods and effects of age of host tissue and temperature

(2011) A. M. Villegas-Fernández et al.   EUROPEAN JOURNAL OF PLANT PATHOLOGY

The Botrytis cinerea phytotoxin botcinic acid requires two polyketide synthases for production and has a redundant role in virulence with botrydial

(2011) BÉRENGÈRE DALMAIS et al.   MOLECULAR PLANT PATHOLOGY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences

(2011) Marnix H. Medema et al.   NUCLEIC ACIDS RESEARCH

Targeted Identification of Short Interspersed Nuclear Element Families Shows Their Widespread Existence and Extreme Heterogeneity in Plant Genomes

(2011) Torsten Wenke et al.   PLANT CELL

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

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

(2011) Joelle Amselem et al.   PLoS Genetics

Botrytis fabiopsis, a new species causing chocolate spot of broad bean in central China

(2010) Jing Zhang et al.   MYCOLOGIA

MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences

(2010) Y. Han et al.   NUCLEIC ACIDS RESEARCH

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

Survival ofBotrytisspp. on infected lentil and chickpea trash in Australia

(2009) K. D. Lindbeck et al.   AUSTRALASIAN PLANT PATHOLOGY

Identification and multi-environment validation of resistance to Botrytis fabae in Vicia faba

(2009) A.M. Villegas-Fernández et al.   FIELD CROPS RESEARCH

Faba bean breeding for disease resistance

(2009) Josefina C. Sillero et al.   FIELD CROPS RESEARCH

Integrated pest management in faba bean

(2009) F.L. Stoddard et al.   FIELD CROPS 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

Structure-based discovery and description of plant and animal Helitrons

(2009) L. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Field screening in Australia of lentil germplasm for resistance to botrytis grey mould

(2008) K. D. Lindbeck et al.   AUSTRALASIAN PLANT PATHOLOGY

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

Survey of chocolate spot (Botrytis fabae) disease of faba bean (Vicia faba L.) and assessment of factors influencing disease epidemics in northern Ethiopia

(2008) Samuel Sahile et al.   CROP PROTECTION

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

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

Effect of mixed cropping and fungicides on chocolate spot (Botrytis fabae) of faba bean (Vicia faba) in Ethiopia

(2007) Samuel Sahile et al.   CROP PROTECTION