Whole-Genome Resequencing and Pan-Transcriptome Reconstruction Highlight the Impact of Genomic Structural Variation on Secondary Metabolite Gene Clusters in the Grapevine Esca Pathogen Phaeoacremonium minimum

Positively Selected Effector Genes and Their Contribution to Virulence in the Smut Fungus Sporisorium reilianum

(2018) Gabriel Schweizer et al.   Genome Biology and Evolution

Managing Grapevine Trunk Diseases With Respect to Etiology and Epidemiology: Current Strategies and Future Prospects

(2018) David Gramaje et al.   PLANT DISEASE

Closed-reference metatranscriptomics enables in planta profiling of putative virulence activities in the grapevine trunk disease complex

(2017) Abraham Morales-Cruz et al.   MOLECULAR PLANT PATHOLOGY

Evolution and genome architecture in fungal plant pathogens

(2017) Mareike Möller et al.   NATURE REVIEWS MICROBIOLOGY

Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast

(2017) Daniel C. Jeffares et al.   Nature Communications

Drivers of genetic diversity in secondary metabolic gene clusters within a fungal species

(2017) Abigail L. Lind et al.   PLOS BIOLOGY

Association Genetics in Plant Pathogens: Minding the Gap between the Natural Variation and the Molecular Function

(2017) Anne Genissel et al.   Frontiers in Plant Science

Are pangenomes adaptive or not?

(2017) Michiel Vos et al.   Nature Microbiology

Assemblytics: a web analytics tool for the detection of variants from an assembly

(2016) Maria Nattestad et al.   BIOINFORMATICS

Microbial interactions: ecology in a molecular perspective

(2016) Raíssa Mesquita Braga et al.   BRAZILIAN JOURNAL OF MICROBIOLOGY

Grapevine pruning systems and cultivars influence the diversity of wood-colonizing fungi

(2016) Renaud Travadon et al.   Fungal Ecology

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

(2016) Luigi Faino et al.   GENOME RESEARCH

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Condition-dependent co-regulation of genomic clusters of virulence factors in the grapevine trunk pathogen Neofusicoccum parvum

(2016) Mélanie Massonnet et al.   MOLECULAR PLANT PATHOLOGY

Biosynthetic investigation of phomopsins reveals a widespread pathway for ribosomal natural products in Ascomycetes

(2016) Wei Ding et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Evolution of Orphan Regions in Genomes of a Fungal Pathogen of Wheat

(2016) Clémence Plissonneau et al.   mBio

Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation

(2016) Minliang Jin et al.   Scientific Reports

Variation in Fumonisin and Ochratoxin Production Associated with Differences in Biosynthetic Gene Content in Aspergillus niger and A. welwitschiae Isolates from Multiple Crop and Geographic Origins

(2016) Antonia Susca et al.   Frontiers in Microbiology

Mildew-Omics: How Global Analyses Aid the Understanding of Life and Evolution of Powdery Mildews

(2016) Laurence V. Bindschedler et al.   Frontiers in Plant Science

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

Distinctive expansion of gene families associated with plant cell wall degradation, secondary metabolism, and nutrient uptake in the genomes of grapevine trunk pathogens

(2015) Abraham Morales-Cruz et al.   BMC GENOMICS

Assessing structural variation in a personal genome—towards a human reference diploid genome

(2015) Adam C English et al.   BMC GENOMICS

SpeedSeq: ultra-fast personal genome analysis and interpretation

(2015) Colby Chiang et al.   NATURE METHODS

The Transporter Classification Database (TCDB): recent advances

(2015) Milton H. Saier et al.   NUCLEIC ACIDS RESEARCH

antiSMASH 3.0—a comprehensive resource for the genome mining of biosynthetic gene clusters

(2015) Tilmann Weber et al.   NUCLEIC ACIDS RESEARCH

Chromosome-level genome map provides insights into diverse defense mechanisms in the medicinal fungus Ganoderma sinense

(2015) Yingjie Zhu et al.   Scientific Reports

Rapidly Evolving Genes Are Key Players in Host Specialization and Virulence of the Fungal Wheat Pathogen Zymoseptoria tritici (Mycosphaerella graminicola)

(2015) Stephan Poppe et al.   PLoS Pathogens

Bacteria in a wood fungal disease: characterization of bacterial communities in wood tissues of esca-foliar symptomatic and asymptomatic grapevines

(2015) Emilie Bruez et al.   Frontiers in Microbiology

Next-generation sequencing approach for connecting secondary metabolites to biosynthetic gene clusters in fungi

(2015) Ralph A. Cacho et al.   Frontiers in Microbiology

Deciphering the Niches of Colonisation of Vitis vinifera L. by the Esca-Associated Fungus Phaeoacremonium aleophilum Using a gfp Marked Strain and Cutting Systems

(2015) Romain Pierron et al.   PLoS One

Genomic Patterns of Positive Selection at the Origin of Rust Fungi

(2015) Diogo N. Silva et al.   PLoS One

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Adaptive genomic structural variation in the grape powdery mildew pathogen, Erysiphe necator

(2014) Laura Jones et al.   BMC GENOMICS

fPoxDB: fungal peroxidase database for comparative genomics

(2014) Jaeyoung Choi et al.   BMC MICROBIOLOGY

Genomic variability as a driver of plant–pathogen coevolution?

(2014) Talia L Karasov et al.   CURRENT OPINION IN PLANT BIOLOGY

Gene Loss Rather Than Gene Gain Is Associated with a Host Jump from Monocots to Dicots in the Smut Fungus Melanopsichium pennsylvanicum

(2014) Rahul Sharma et al.   Genome Biology and Evolution

Insights into the Maize Pan-Genome and Pan-Transcriptome

(2014) C. N. Hirsch et al.   PLANT CELL

The Evolution of Fungal Metabolic Pathways

(2014) Jennifer H. Wisecaver et al.   PLoS Genetics

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

Detecting Natural Selection in Genomic Data

(2013) Joseph J. Vitti et al.   Annual Review of Genetics

Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici reveal polymorphic and haustorial expressed secreted proteins as candidate effectors

(2013) Dario Cantu et al.   BMC GENOMICS

Genomic clustering and co-regulation of transcriptional networks in the pathogenic fungus Fusarium graminearum

(2013) Katherine Lawler et al.   BMC Systems Biology

Birth, death and horizontal transfer of the fumonisin biosynthetic gene cluster during the evolutionary diversification ofFusarium

(2013) Robert H. Proctor et al.   MOLECULAR MICROBIOLOGY

A novel Fomitiporia species associated with esca on grapevine in South Africa

(2013) M. Cloete et al.   MYCOLOGICAL PROGRESS

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

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

High genotypic and virulence diversity inIlyonectria liriodendriisolates associated with black foot disease in New Zealand vineyards

(2013) B. Pathrose et al.   PLANT PATHOLOGY

Virulence affected by assay parameters during grapevine pathogenicity studies with Botryosphaeriaceae nursery isolates

(2013) R. Billones-Baaijens et al.   PLANT PATHOLOGY

Diversity and abundance of phosphonate biosynthetic genes in nature

(2013) X. Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

The Evolutionary Imprint of Domestication on Genome Variation and Function of the Filamentous Fungus Aspergillus oryzae

(2012) John G. Gibbons et al.   CURRENT BIOLOGY

Genetic and virulence diversity, and mating type distribution of Togninia minima causing grapevine trunk diseases in Spain

(2012) D. Gramaje et al.   EUROPEAN JOURNAL OF PLANT PATHOLOGY

Genes under positive selection in a model plant pathogenic fungus, Botrytis

(2012) Gabriela Aguileta et al.   INFECTION GENETICS AND EVOLUTION

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

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

Identification and Characterization of the Echinocandin B Biosynthetic Gene Cluster from Emericella rugulosa NRRL 11440

(2012) Ralph A. Cacho et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Microevolution of Cryptococcus neoformans Driven by Massive Tandem Gene Amplification

(2012) E. W. L. Chow et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Sylvain Raffaele et al.   NATURE REVIEWS MICROBIOLOGY

Regulation of fungal secondary metabolism

(2012) Axel A. Brakhage   NATURE REVIEWS MICROBIOLOGY

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

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

Pathogenicity of Diatrypaceous Fungi on Grapevines in Australia

(2012) Wayne M. Pitt et al.   PLANT DISEASE

Maize (Zea mays L.) Genome Diversity as Revealed by RNA-Sequencing

(2012) Candice N. Hansey et al.   PLoS One

The making of a new pathogen: Insights from comparative population genomics of the domesticated wheat pathogen Mycosphaerella graminicola and its wild sister species

(2011) E. H. Stukenbrock et al.   GENOME RESEARCH

Fungal Indole Alkaloid Biosynthesis: Genetic and Biochemical Investigation of the Tryptoquialanine Pathway inPenicillium aethiopicum

(2011) Xue Gao et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

A comprehensive phylogeny of Neurospora reveals a link between reproductive mode and molecular evolution in fungi

(2011) Kristiina Nygren et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

A Comprehensive Analysis of Genes Encoding Small Secreted Proteins Identifies Candidate Effectors inMelampsora larici-populina(Poplar Leaf Rust)

(2011) Stéphane Hacquard et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

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

Phytotoxins Produced by Fungi Associated with Grapevine Trunk Diseases

(2011) Anna Andolfi et al.   Toxins

Nonlinear Biosynthetic Gene Cluster Dose Effect on Penicillin Production by Penicillium chrysogenum

(2010) J. G. Nijland et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Recent advancements in the biosynthetic mechanisms for polyketide-derived mycotoxins

(2010) Justin Huffman et al.   BIOPOLYMERS

Identification of the Viridicatumtoxin and Griseofulvin Gene Clusters from Penicillium aethiopicum

(2010) Yit-Heng Chooi et al.   CHEMISTRY & BIOLOGY

Diversification and evolution of the avirulence gene AVR-Pita1 in field isolates of Magnaporthe oryzae

(2010) Yuntao Dai et al.   FUNGAL GENETICS AND BIOLOGY

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

(2010) A. McKenna et al.   GENOME RESEARCH

Finding candidate genes under positive selection in Non-model species: examples of genes involved in host specialization in pathogens

(2010) G. AGUILETA et al.   MOLECULAR ECOLOGY

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Chemistry and Biology of Mycotoxins and Related Fungal Metabolites

(2009) Stefan Bräse et al.   CHEMICAL REVIEWS

Esca et Black Dead Arm : deux acteurs majeurs des maladies du bois chez la Vigne

(2009) Philippe Larignon et al.   COMPTES RENDUS BIOLOGIES

Copy Number Variation and Transcriptional Polymorphisms of Phytophthora sojae RXLR Effector Genes Avr1a and Avr3a

(2009) Dinah Qutob et al.   PLoS One

Efflux in Fungi: La Pièce de Résistance

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

Secondary metabolism: regulation and role in fungal biology

(2008) Ellen M Fox et al.   CURRENT OPINION IN MICROBIOLOGY

Assessing the gene space in draft genomes

(2008) Genis Parra et al.   NUCLEIC ACIDS RESEARCH

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

(2008) Brian J Haas et al.   GENOME BIOLOGY