Increased virulence of Puccinia coronata f. sp.avenae populations through allele frequency changes at multiple putative Avr loci

Evolution of virulence in rust fungi — multiple solutions to one problem

(2020) Melania Figueroa et al.   CURRENT OPINION IN PLANT BIOLOGY

Selective Sweeps

(2019) Wolfgang Stephan   GENETICS

Virulence of Puccinia coronata var avenae f. sp. avenae (oat crown rust) in Canada during 2010 to 2015

(2019) James G. Menzies et al.   CANADIAN JOURNAL OF PLANT PATHOLOGY

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Genomic insights from the first chromosome-scale assemblies of oat (Avena spp.) diploid species

(2019) Peter J. Maughan et al.   BMC BIOLOGY

Emergence of the Ug99 lineage of the wheat stem rust pathogen through somatic hybridisation

(2019) Feng Li et al.   Nature Communications

Populations of Phytophthora rubi Show Little Differentiation and High Rates of Migration Among States in the Western United States

(2018) Javier F. Tabima et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

De Novo Assembly and Phasing of Dikaryotic Genomes from Two Isolates of Puccinia coronata f. sp. avenae, the Causal Agent of Oat Crown Rust

(2018) Marisa E. Miller et al.   mBio

D-GENIES: dot plot large genomes in an interactive, efficient and simple way

(2018) Floréal Cabanettes et al.   PeerJ

Diversity of oat crown rust (Puccinia coronata f.sp. avenae) isolates detected by virulence and AFLP analyses

(2018) H. Klenová-Jiráková et al.   PLANT PROTECTION SCIENCE

Mapping of crown rust resistance gene Pc53 in oat (Avena sativa)

(2018) Belayneh Admassu-Yimer et al.   PLoS One

Puccinia coronata f. sp. avenae : a threat to global oat production

(2017) Eric S. Nazareno et al.   MOLECULAR PLANT PATHOLOGY

Evolution and genome architecture in fungal plant pathogens

(2017) Mareike Möller et al.   NATURE REVIEWS MICROBIOLOGY

Variation in theAvrSr35gene determinesSr35resistance against wheat stem rust race Ug99

(2017) Andres Salcedo et al.   SCIENCE

Loss ofAvrSr50by somatic exchange in stem rust leads to virulence forSr50resistance in wheat

(2017) Jiapeng Chen et al.   SCIENCE

kWIP: The k-mer weighted inner product, a de novo estimator of genetic similarity

(2017) Kevin D. Murray et al.   PLoS Computational Biology

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

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

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

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

A Consensus Map in Cultivated Hexaploid Oat Reveals Conserved Grass Synteny with Substantial Subgenome Rearrangement

(2016) Ashley S. Chaffin et al.   Plant Genome

Changing the Game: Using Integrative Genomics to Probe Virulence Mechanisms of the Stem Rust Pathogen Puccinia graminis f. sp. tritici

(2016) Melania Figueroa et al.   Frontiers in Plant Science

Comparative genomics of Australian isolates of the wheat stem rust pathogen Puccinia graminis f. sp. tritici reveals extensive polymorphism in candidate effector genes

(2015) Narayana M. Upadhyaya et al.   Frontiers in Plant Science

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

UpSet: Visualization of Intersecting Sets

(2014) Alexander Lex et al.   IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS

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

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

These Are Not the K-mers You Are Looking For: Efficient Online K-mer Counting Using a Probabilistic Data Structure

(2014) Qingpeng Zhang et al.   PLoS One

Effector proteins of rust fungi

(2014) Benjamin Petre et al.   Frontiers in Plant Science

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

(2014) Zhian N. Kamvar et al.   PeerJ

The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine

(2013) Kentaro Yoshida et al.   eLife

GAPIT: genome association and prediction integrated tool

(2012) Alexander E. Lipka et al.   BIOINFORMATICS

ggbio: an R package for extending the grammar of graphics for genomic data

(2012) Tengfei Yin et al.   GENOME BIOLOGY

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

(2011) Thibaut Jombart et al.   BIOINFORMATICS

Virulence ofPuccinia coronataf. sp.avenaein the Eastern Prairie Region of Canada during 2007–2009

(2011) James Chong et al.   CANADIAN JOURNAL OF PLANT PATHOLOGY

The genetic structure of the plant pathogenic fungus Melampsora larici-populina on its wild host is extensively impacted by host domestication

(2011) C. XHAARD et al.   MOLECULAR ECOLOGY

Virulence in Oat Crown Rust (Puccinia coronata f. sp. avenae) in the United States from 2006 through 2009

(2011) M. L. Carson   PLANT DISEASE

Next Generation Sequencing Provides Rapid Access to the Genome of Puccinia striiformis f. sp. tritici, the Causal Agent of Wheat Stripe Rust

(2011) Dario Cantu et al.   PLoS One

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Mixed linear model approach adapted for genome-wide association studies

(2010) Zhiwu Zhang et al.   NATURE GENETICS

Plant immunity: towards an integrated view of plant–pathogen interactions

(2010) Peter N. Dodds et al.   NATURE REVIEWS GENETICS

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Diversity and Evolution of Effector Loci in Natural Populations of the Plant Pathogen Melampsora lini

(2009) L. G. Barrett et al.   MOLECULAR BIOLOGY AND EVOLUTION

Crown Rust Development and Selection for Virulence inPuccinia coronataf. sp.avenaein an Oat Multiline Cultivar

(2009) M. L. Carson   PLANT DISEASE

adegenet: a R package for the multivariate analysis of genetic markers

(2008) Thibaut Jombart   BIOINFORMATICS

Virulence Frequencies in Oat Crown Rust in the United States from 2001 Through 2005

(2008) M. L. Carson   PLANT DISEASE

Breeding cereals for rust resistance in Australia

(2008) R. F. Park   PLANT PATHOLOGY