De Novo Genome Assembly and Comparative Genomics of the Barley Leaf Rust Pathogen Puccinia hordei Identifies Candidates for Three Avirulence Genes

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

A Near-Complete Haplotype-Phased Genome of the Dikaryotic Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici Reveals High Interhaplotype Diversity

(2018) Benjamin Schwessinger et al.   mBio

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

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

Regulatory Shifts in Plastid Transcription Play a Key Role in Morphological Conversions of Plastids during Plant Development

(2017) Monique Liebers et al.   Frontiers in Plant Science

Comparative Genomics Integrated with Association Analysis Identifies Candidate Effector Genes Corresponding to Lr20 in Phenotype-Paired Puccinia triticina Isolates from Australia

(2017) Jing Qin Wu et al.   Frontiers in Plant Science

Genome analysis and avirulence gene cloning using a high-density RADseq linkage map of the flax rust fungus, Melampsora lini

(2016) Claire Anderson et al.   BMC GENOMICS

AvrPm2 encodes an RNase-like avirulence effector which is conserved in the two different specialized forms of wheat and rye powdery mildew fungus

(2016) Coraline R. Praz et al.   NEW PHYTOLOGIST

Allelic barley MLA immune receptors recognize sequence-unrelated avirulence effectors of the powdery mildew pathogen

(2016) Xunli Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative Analysis Highlights Variable Genome Content of Wheat Rusts and Divergence of the Mating Loci

(2016) Christina A. Cuomo et al.   G3-Genes Genomes Genetics

Computational Prediction of Effector Proteins in Fungi: Opportunities and Challenges

(2016) Humira Sonah et al.   Frontiers in Plant Science

Leaf Rust of Cultivated Barley: Pathology and Control

(2015) Robert F. Park et al.   Annual Review of Phytopathology

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

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

Evaluation of Secretion Prediction Highlights Differing Approaches Needed for Oomycete and Fungal Effectors

(2015) Jana Sperschneider et al.   Frontiers in Plant Science

Transcriptome Sequencing Uncovers the Avr5 Avirulence Gene of the Tomato Leaf Mold Pathogen Cladosporium fulvum

(2014) Carl H. Mesarich et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

The Ins and Outs of Rust Haustoria

(2014) Diana P. Garnica et al.   PLoS Pathogens

The genome sequence and effector complement of the flax rust pathogen Melampsora lini

(2014) Adnane Nemri et al.   Frontiers in Plant Science

Isolation and characterization of microsatellite markers for the causal agent of barley leaf rust, Puccinia hordei

(2013) H. Karaoglu et al.   AUSTRALASIAN PLANT PATHOLOGY

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

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

MCMC-ODPR: Primer design optimization using Markov Chain Monte Carlo sampling

(2012) James L Kitchen et al.   BMC BIOINFORMATICS

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

(2012) Pablo Cingolani et al.   FLY

MSDB: A User-Friendly Program for Reporting Distribution and Building Databases of Microsatellites from Genome Sequences

(2012) Lianming Du et al.   JOURNAL OF HEREDITY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Barley Stripe Mosaic Virus-Mediated Tools for Investigating Gene Function in Cereal Plants and Their Pathogens: Virus-Induced Gene Silencing, Host-Mediated Gene Silencing, and Virus-Mediated Overexpression of Heterologous Protein

(2012) W.-S. Lee et al.   PLANT PHYSIOLOGY

Using Hierarchical Clustering of Secreted Protein Families to Classify and Rank Candidate Effectors of Rust Fungi

(2012) Diane G. O. Saunders et al.   PLoS One

Tomato immune receptor Ve1 recognizes effector of multiple fungal pathogens uncovered by genome and RNA sequencing

(2012) R. de Jonge et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Obligate biotrophy features unraveled by the genomic analysis of rust fungi

(2011) S. Duplessis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) A. McKenna et al.   GENOME RESEARCH

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

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