Whole‐genome sequencing elucidates the species‐wide diversity and evolution of fungicide resistance in the early blight pathogen Alternaria solani

Temperature drives contrasting Alternaria Leaf Spot epidemic development in canola and mustard rape from Alternaria japonica and A. brassicae

(2020) Hebba F.D. Al-lami et al.   PLANT DISEASE

Gene Genealogies Reveal High Nucleotide Diversity and Admixture Haplotypes within Three Alternaria Species Associated with Tomato and Potato

(2020) Tika Adhikari et al.   PHYTOPATHOLOGY

The proportion of soil-borne pathogens increases with warming at the global scale

(2020) Manuel Delgado-Baquerizo et al.   Nature Climate Change

Making sense of Integrated Pest Management (IPM) in the light of evolution

(2020) Kristina Karlsson Green et al.   Evolutionary Applications

Spatiotemporal Distribution of Potato-Associated Alternaria Species in Wisconsin

(2020) Shunping Ding et al.   PLANT DISEASE

The complex genomic basis of rapid convergent adaptation to pesticides across continents in a fungal plant pathogen

(2020) Fanny E. Hartmann et al.   MOLECULAR ECOLOGY

Population Genomics of Filamentous Plant Pathogens—A Brief Overview of Research Questions, Approaches, and Pitfalls

(2020) Sydney Everhart et al.   PHYTOPATHOLOGY

Genetic Diversity and Structure in Regional Cercospora beticola Populations from Beta vulgaris ssp. vulgaris Suggest Two Clusters of Separate Origin

(2019) Noel Knight et al.   PHYTOPATHOLOGY

RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference

(2019) Alexey M Kozlov et al.   BIOINFORMATICS

Long term field sampling in Sweden reveals a shift in occurrence of cytochrome b genotype and amino acid substitution F129L in Alternaria solani, together with a high incidence of the G143A substitution in Alternaria alternata

(2019) E. Edin et al.   EUROPEAN JOURNAL OF PLANT PATHOLOGY

QoI Fungicide Resistance Mutations in Alternaria solani and Alternaria alternata are Fully Established in Potato Growing Areas in Bavaria and Dual Resistance against SDHI Fungicides is Upcoming

(2019) Mathias Nottensteiner et al.   Gesunde Pflanzen

The current epidemic of the barley pathogen Ramularia collo-cygni derives from a recent population expansion and shows global admixture

(2019) Remco Stam et al.   PHYTOPATHOLOGY

Occurrence of sdh mutations in German Alternaria solani isolates and potential impact on boscalid sensitivity in vitro, in the greenhouse and in the field

(2019) Nicole Metz et al.   PLANT DISEASE

Within-season changes in Alternaria solani populations in potato in response to fungicide application strategies

(2019) Firuz Odilbekov et al.   EUROPEAN JOURNAL OF PLANT PATHOLOGY

Treeio: An R Package for Phylogenetic Tree Input and Output with Richly Annotated and Associated Data

(2019) Li-Gen Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Induced expression of CYP51 associated with difenoconazole resistance in the pathogenic Alternaria sect. on potato in China

(2019) Yue Zhang et al.   PEST MANAGEMENT SCIENCE

Population structure and frequency differences of CYP51 mutations in Zymoseptoria tritici populations in the Nordic and Baltic regions

(2018) Nana Vagndorf et al.   EUROPEAN JOURNAL OF PLANT PATHOLOGY

Gapless Genome Assembly of the Potato and Tomato Early Blight Pathogen Alternaria solani

(2018) Pieter J. Wolters et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Spatial and Temporal Distribution of Mutations Conferring QoI and SDHI Resistance in Alternaria solani Across the United States

(2018) Mitchell J. Bauske et al.   PLANT DISEASE

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

(2018) Pierre Gladieux et al.   mBio

Diversity Assessment Among Alternaria solani Isolates Causing Early Blight of Tomato in India

(2018) Priti Upadhyay et al.   Proceedings of the National Academy of Sciences, India. Section B

Changes in field dose-response curves for demethylation inhibitor (DMI) and quinone outside inhibitor (QoI) fungicides against Zymoseptoria tritici , related to laboratory sensitivity phenotyping and genotyping assays

(2017) Jonathan J Blake et al.   PEST MANAGEMENT SCIENCE

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

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

Alternaria species associated with early blight epidemics on tomato and other Solanaceae crops in northwestern Algeria

(2016) Nabahat Bessadat et al.   EUROPEAN JOURNAL OF PLANT PATHOLOGY

vcfr: a package to manipulate and visualize variant call format data in R

(2016) Brian J. Knaus et al.   Molecular Ecology Resources

Mutations in the CYP51 gene reduce DMI sensitivity in Parastagonospora nodorum populations in Europe and China

(2016) Danilo AS Pereira et al.   PEST MANAGEMENT SCIENCE

Identification and Enumeration of Small-Spored Alternaria Species Associated with Potato in the U.S. Northwest

(2016) Lydia S. Tymon et al.   PLANT DISEASE

Local adaptation to temperature in populations and clonal lineages of the Irish potato famine pathogenPhytophthora infestans

(2016) Nicolas Mariette et al.   Ecology and Evolution

Genetic diversity and occurrence of the F129L substitutions among isolates of Alternaria solani in south-eastern Sweden

(2016) Firuz Odilbekov et al.   HEREDITAS

Genetic variability among Alternaria solani isolates from potatoes in Southern Germany based on RAPD-profiles

(2016) Jürgen H. Leiminger et al.   Journal of Plant Diseases and Protection

LEA: AnRpackage for landscape and ecological association studies

(2015) Eric Frichot et al.   Methods in Ecology and Evolution

Population genetic analysis reveals cryptic sex in the phytopathogenic fungus Alternaria alternata

(2015) Jing-Wen Meng et al.   Scientific Reports

Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality

(2015) Zhian N. Kamvar et al.   Frontiers in Genetics

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Untersuchungen zur Befallsentwicklung und Ertragswirkung der Dürrfleckenkrankheit (Alternaria spp.) in Kartoffelsorten unterschiedlicher Reifegruppe

(2014) Jürgen H. Leiminger et al.   Gesunde Pflanzen

PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

(2014) Bastian Pfeifer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction

(2014) Zhian N. Kamvar et al.   PeerJ

Molecular Characterization and Detection of Mutations Associated with Resistance to Succinate Dehydrogenase-Inhibiting Fungicides in Alternaria solani

(2013) I. Mallik et al.   PHYTOPATHOLOGY

First Report of Alternaria Blight of Potato Caused by Alternaria tenuissima in China

(2013) H. H. Zheng et al.   PLANT DISEASE

Alternaria redefined

(2013) J.H.C. Woudenberg et al.   STUDIES IN MYCOLOGY

A high-performance computing toolset for relatedness and principal component analysis of SNP data

(2012) X. Zheng et al.   BIOINFORMATICS

Analysis of genetic and pathogenic variation of Alternaria solani from a potato production region

(2012) Brooke Weber et al.   EUROPEAN JOURNAL OF PLANT PATHOLOGY

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

(2012) Pablo Cingolani et al.   FLY

Genome-Wide Fine-Scale Recombination Rate Variation in Drosophila melanogaster

(2012) Andrew H. Chan et al.   PLoS Genetics

Using Drosophila melanogaster as a Model for Genotoxic Chemical Mutational Studies with a New Program, SnpSift

(2012) Pablo Cingolani et al.   Frontiers in Genetics

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Absence of isolation by distance patterns at the regional scale in the fungal plant pathogen Leptosphaeria maculans

(2011) Renaud Travadon et al.   Fungal Biology

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

(2011) Mark A DePristo et al.   NATURE GENETICS

Early Blight Control in Potato Using Disease-Orientated Threshold Values

(2011) J. H. Leiminger et al.   PLANT DISEASE

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

(2010) A. McKenna et al.   GENOME RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS