Long-Read–Based de novo Genome Assembly and Comparative Genomics of the Wheat Leaf Rust Pathogen Puccinia triticina Identifies Candidates for Three Avirulence Genes

The global burden of pathogens and pests on major food crops

(2019) Serge Savary et al.   Nature Ecology & Evolution

The AvrPm3-Pm3 effector-NLR interactions control both race-specific resistance and host-specificity of cereal mildews on wheat

(2019) Salim Bourras et al.   Nature Communications

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

(2019) Jiapeng Chen et al.   G3-Genes Genomes Genetics

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

A Deubiquitinating Enzyme Ubp14 Is Required for Development, Stress Response, Nutrient Utilization, and Pathogenesis of Magnaporthe oryzae

(2018) Zhao Wang et al.   Frontiers in Microbiology

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies

(2018) Michael J. Roach et al.   BMC BIOINFORMATICS

Two Methods for Mapping and Visualizing Associated Data on Phylogeny Using Ggtree

(2018) Guangchuang Yu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Advances in understanding obligate biotrophy in rust fungi

(2018) Cécile Lorrain et al.   NEW PHYTOLOGIST

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

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

Phylogenomic evolutionary surveys of subtilase superfamily genes in fungi

(2017) Juan Li et al.   Scientific Reports

Regulation of proteinaceous effector expression in phytopathogenic fungi

(2017) Kar-Chun Tan et al.   PLoS Pathogens

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-Wide Association Studies In Plant Pathosystems: Toward an Ecological Genomics Approach

(2017) Claudia Bartoli et al.   Frontiers in Plant Science

Dissection of genomic features and variations of three pathotypes of Puccinia striiformis through whole genome sequencing

(2017) Kanti Kiran et al.   Scientific Reports

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

Draft Genome of the Wheat Rust Pathogen (Puccinia triticina)Unravels Genome-Wide Structural Variations during Evolution

(2016) Kanti Kiran et al.   Genome Biology and Evolution

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

(2016) Todd M. Lowe et al.   NUCLEIC ACIDS RESEARCH

Putative Rust Fungal Effector Proteins in Infected Bean and Soybean Leaves

(2016) Bret Cooper et al.   PHYTOPATHOLOGY

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

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS: Table 1.

(2015) Katharina J. Hoff et al.   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

The Hitchhiker’s guide to Hi-C analysis: Practical guidelines

(2015) Bryan R. Lajoie et al.   METHODS

Twenty years of theMEROPSdatabase of proteolytic enzymes, their substrates and inhibitors

(2015) Neil D. Rawlings et al.   NUCLEIC ACIDS RESEARCH

Proteome of monoclonal antibody-purified haustoria fromPuccinia triticinaRace-1

(2015) Christof Rampitsch et al.   PROTEOMICS

Advances and Challenges in Computational Prediction of Effectors from Plant Pathogenic Fungi

(2015) Jana Sperschneider et al.   PLoS Pathogens

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

Extracellular peptidases of the cereal pathogen Fusarium graminearum

(2015) Rohan G. T. Lowe et al.   Frontiers in Plant Science

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

VariantAnnotation: a Bioconductor package for exploration and annotation of genetic variants

(2014) V. Obenchain et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Using transcription of six Puccinia triticina races to identify the effective secretome during infection of wheat

(2014) Myron Bruce et al.   Frontiers in Plant Science

Conserved loci of leaf and stem rust fungi of wheat share synteny interrupted by lineage-specific influx of repeat elements

(2013) John P Fellers et al.   BMC GENOMICS

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

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

High genome heterozygosity and endemic genetic recombination in the wheat stripe rust fungus

(2013) Wenming Zheng et al.   Nature Communications

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

dbCAN: a web resource for automated carbohydrate-active enzyme annotation

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

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

Revision of the Nomenclature of the Differential Host-Pathogen Interactions of Venturia inaequalis and Malus

(2011) Vincent G.M. Bus et al.   Annual Review of Phytopathology

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi

(2011) Junhuan Xu et al.   BMC GENOMICS

Global status of wheat leaf rust caused by Puccinia triticina

(2011) J. Huerta-Espino et al.   EUPHYTICA

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

Proteome analysis of wheat leaf rust fungus, Puccinia triticina, infection structures enriched for haustoria

(2011) Xiao Song et al.   PROTEOMICS

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

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY