Coexistence of Multiple Endemic and Pandemic Lineages of the Rice Blast Pathogen

The rice paradox: Multiple origins but single domestication in Asian rice

(2017) Jae Young Choi et al.   MOLECULAR BIOLOGY AND EVOLUTION

Emergence of wheat blast in Bangladesh was caused by a South American lineage of Magnaporthe oryzae

(2016) M. Tofazzal Islam et al.   BMC BIOLOGY

Host specialization of the blast fungus Magnaporthe oryzae is associated with dynamic gain and loss of genes linked to transposable elements

(2016) Kentaro Yoshida et al.   BMC GENOMICS

PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses

(2016) Robert Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferences from tip-calibrated phylogenies: a review and a practical guide

(2016) Adrien Rieux et al.   MOLECULAR ECOLOGY

Evolution of Compatibility Range in the Rice−Magnaporthe oryzaeSystem: An Uneven Distribution of R Genes Between Rice Subspecies

(2016) Romain Gallet et al.   PHYTOPATHOLOGY

Pathogen effectors and plant immunity determine specialization of the blast fungus to rice subspecies

(2016) Jingjing Liao et al.   eLife

Deciphering Genome Content and Evolutionary Relationships of Isolates from the FungusMagnaporthe oryzaeAttacking Different Host Plants

(2015) Hélène Chiapello et al.   Genome Biology and Evolution

Genomic Characterization of a South AmericanPhytophthoraHybrid Mandates Reassessment of the Geographic Origins ofPhytophthora infestans

(2015) Michael D. Martin et al.   MOLECULAR BIOLOGY AND EVOLUTION

The population biology of fungal invasions

(2015) P. Gladieux et al.   MOLECULAR ECOLOGY

Short Tree, Long Tree, Right Tree, Wrong Tree: New Acquisition Bias Corrections for Inferring SNP Phylogenies

(2015) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

Structure Analysis Uncovers a Highly Diverse but Structurally Conserved Effector Family in Phytopathogenic Fungi

(2015) Karine de Guillen et al.   PLoS Pathogens

Rice domestication occurred through single origin and multiple introgressions

(2015) Xuehui Huang et al.   Nature Plants

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Diversity and Variability of NOD-Like Receptors in Fungi

(2014) Witold Dyrka et al.   Genome Biology and Evolution

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

(2014) Kevin Cheeseman et al.   Nature Communications

Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes

(2013) Pierre Gladieux et al.   MOLECULAR ECOLOGY

Inferring the contribution of sexual reproduction, migration and off-season survival to the temporal maintenance of microbial populations: a case study on the wheat fungal pathogenPuccinia striiformisf.sp.tritici

(2013) Sajid Ali et al.   MOLECULAR ECOLOGY

South-East Asia is the center of origin, diversity and dispersion of the rice blast fungus,Magnaporthe oryzae

(2013) Dounia Saleh et al.   NEW PHYTOLOGIST

EggLib: processing, analysis and simulation tools for population genetics and genomics

(2012) Stéphane De Mita et al.   BMC GENETICS

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

(2012) Pablo Cingolani et al.   FLY

Weak Selection and Protein Evolution

(2012) H. Akashi et al.   GENETICS

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sex at the origin: an Asian population of the rice blast fungusMagnaporthe oryzaereproduces sexually

(2012) DOUNIA SALEH et al.   MOLECULAR ECOLOGY

A map of rice genome variation reveals the origin of cultivated rice

(2012) Xuehui Huang et al.   NATURE

Inference of Population Structure using Dense Haplotype Data

(2012) Daniel John Lawson et al.   PLoS Genetics

A Population Genomics Perspective on the Emergence and Adaptation of New Plant Pathogens in Agro-Ecosystems

(2012) Eva H. Stukenbrock et al.   PLoS Pathogens

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

adegenet 1.3-1: new tools for the analysis of genome-wide SNP data

(2011) Thibaut Jombart et al.   BIOINFORMATICS

Nuclear and Genome Dynamics in Multinucleate Ascomycete Fungi

(2011) Marcus Roper et al.   CURRENT BIOLOGY

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

Population genomics and local adaptation in wild isolates of a model microbial eukaryote

(2011) C. E. Ellison et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A molecular evolutionary concept connecting nonhost resistance, pathogen host range, and pathogen speciation

(2011) Paul Schulze-Lefert et al.   TRENDS IN PLANT SCIENCE

Low Diversity Cryptococcus neoformans Variety grubii Multilocus Sequence Types from Thailand Are Consistent with an Ancestral African Origin

(2011) Sitali P. Simwami et al.   PLoS Pathogens

The rise and rise of emerging infectious fungi challenges food security and ecosystem health

(2011) Sarah Gurr et al.   Fungal Biology Reviews

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

(2010) A. McKenna et al.   GENOME RESEARCH

Linking the emergence of fungal plant diseases with ecological speciation

(2010) Tatiana Giraud et al.   TRENDS IN ECOLOGY & EVOLUTION

Evidence that Adaptation in Drosophila Is Not Limited by Mutation at Single Sites

(2010) Talia Karasov et al.   PLoS Genetics

Consilience of genetics and archaeobotany in the entangled history of rice

(2010) Dorian Q. Fuller et al.   Archaeological and Anthropological Sciences

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Inferring weak population structure with the assistance of sample group information

(2009) MELISSA J. HUBISZ et al.   Molecular Ecology Resources

A comparative view of the evolution of grasses under domestication

(2009) Sylvain Glémin et al.   NEW PHYTOLOGIST

Linkage Disequilibrium Decay and Haplotype Block Structure in the Pig

(2008) A. J. Amaral et al.   GENETICS