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

Insights from the genome of a high alkaline cellulase producing Aspergillus fumigatus strain obtained from Peruvian Amazon rainforest

(2017) Sujay Paul et al.   JOURNAL OF BIOTECHNOLOGY

Genome sequence ofAspergillus luchuensisNBRC 4314

(2016) Osamu Yamada et al.   DNA RESEARCH

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Secondary metabolite arsenal of an opportunistic pathogenic fungus

(2016) Elaine Bignell et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Small genome of the fungusEscovopsis weberi, a specialized disease agent of ant agriculture

(2016) Tom J. B. de Man et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Survival trade-offs in plant roots during colonization by closely related beneficial and pathogenic fungi

(2016) Stéphane Hacquard et al.   Nature Communications

The completed genome sequence of the pathogenic ascomycete fungus Fusarium graminearum

(2015) Robert King et al.   BMC GENOMICS

Genome Sequencing of Multiple Isolates Highlights Subtelomeric Genomic Diversity withinFusarium fujikuroi

(2015) Matteo Chiara et al.   Genome Biology and Evolution

Translating biosynthetic gene clusters into fungal armor and weaponry

(2015) Nancy P Keller   Nature Chemical Biology

Examining the Evolution of the Regulatory Circuit Controlling Secondary Metabolism and Development in the Fungal Genus Aspergillus

(2015) Abigail L. Lind et al.   PLoS Genetics

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Multiple recent horizontal transfers of a large genomic region in cheese making fungi

(2014) Kevin Cheeseman et al.   Nature Communications

Human and Plant Fungal Pathogens: The Role of Secondary Metabolites

(2014) Daniel H. Scharf et al.   PLoS Pathogens

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Comprehensive annotation of secondary metabolite biosynthetic genes and gene clusters of Aspergillus nidulans, A. fumigatus, A. niger and A. oryzae

(2013) Diane O Inglis et al.   BMC MICROBIOLOGY

The Fumagillin Biosynthetic Gene Cluster in Aspergillus fumigatus Encodes a Cryptic Terpene Cyclase Involved in the Formation of β-trans-Bergamotene

(2013) Hsiao-Ching Lin et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

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

Horizontal gene transfer in osmotrophs: playing with public goods

(2013) Thomas A. Richards et al.   NATURE REVIEWS MICROBIOLOGY

A Functional Bikaverin Biosynthesis Gene Cluster in Rare Strains of Botrytis cinerea Is Positively Controlled by VELVET

(2013) Julia Schumacher et al.   PLoS One

Prototype of an intertwined secondary-metabolite supercluster

(2013) P. Wiemann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Resequencing and Comparative Genomics of Stagonospora nodorum : Sectional Gene Absence and Effector Discovery

(2013) Robert Andrew Syme et al.   G3-Genes Genomes Genetics

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

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

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

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

Horizontal Transfer and Death of a Fungal Secondary Metabolic Gene Cluster

(2012) Matthew A. Campbell et al.   Genome Biology and Evolution

Two Different Secondary Metabolism Gene Clusters Occupied the Same Ancestral Locus in Fungal Dermatophytes of the Arthrodermataceae

(2012) Han Zhang et al.   PLoS One

Genome Sequence of the White Koji Mold Aspergillus kawachii IFO 4308, Used for Brewing the Japanese Distilled Spirit Shochu

(2011) Taiki Futagami et al.   EUKARYOTIC CELL

Comparative genomics of citric-acid-producing Aspergillus niger ATCC 1015 versus enzyme-producing CBS 513.88

(2011) M. R. Andersen et al.   GENOME RESEARCH

Targeted Disruption of Nonribosomal Peptide Synthetasepes3Augments the Virulence of Aspergillus fumigatus

(2011) Karen A. O'Hanlon et al.   INFECTION AND IMMUNITY

Thermostable cellulase production of Aspergillus fumigatus Z5 under solid-state fermentation and its application in degradation of agricultural wastes

(2011) Dongyang Liu et al.   INTERNATIONAL BIODETERIORATION & BIODEGRADATION

On the trail of a cereal killer: recent advances in Fusarium graminearum pathogenomics and host resistance

(2011) KEMAL KAZAN et al.   MOLECULAR PLANT PATHOLOGY

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

(2011) Mark A DePristo et al.   NATURE GENETICS

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

Multiple Means to the Same End: The Genetic Basis of Acquired Stress Resistance in Yeast

(2011) David B. Berry et al.   PLoS Genetics

Genome Sequencing and Comparative Transcriptomics of the Model Entomopathogenic Fungi Metarhizium anisopliae and M. acridum

(2011) Qiang Gao et al.   PLoS Genetics

Metabolomic Analysis and Visualization Engine for LC−MS Data

(2010) Eugene Melamud et al.   ANALYTICAL CHEMISTRY

Phylogenomics reveals subfamilies of fungal nonribosomal peptide synthetases and their evolutionary relationships

(2010) Kathryn E Bushley et al.   BMC EVOLUTIONARY BIOLOGY

Horizontal Transfer of a Large and Highly Toxic Secondary Metabolic Gene Cluster between Fungi

(2010) Jason C. Slot et al.   CURRENT BIOLOGY

Secondary metabolism in fungi: does chromosomal location matter?

(2010) Jonathan M Palmer et al.   CURRENT OPINION IN MICROBIOLOGY

SMURF: Genomic mapping of fungal secondary metabolite clusters

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

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Evidence that a secondary metabolic biosynthetic gene cluster has grown by gene relocation during evolution of the filamentous fungusFusarium

(2009) Robert H. Proctor et al.   MOLECULAR MICROBIOLOGY

Secondary metabolism: regulation and role in fungal biology

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

A fumonisin biosynthetic gene cluster in Fusarium oxysporum strain O-1890 and the genetic basis for B versus C fumonisin production

(2008) Robert H. Proctor et al.   FUNGAL GENETICS AND BIOLOGY

A universal classification of eukaryotic transposable elements implemented in Repbase

(2008) Vladimir V. Kapitonov et al.   NATURE REVIEWS GENETICS

Genomic Islands in the Pathogenic Filamentous Fungus Aspergillus fumigatus

(2008) Natalie D. Fedorova et al.   PLoS Genetics

Evidence for horizontal transfer of a secondary metabolite gene cluster between fungi

(2008) Nora Khaldi et al.   GENOME BIOLOGY