Genomic insights into host adaptation between the wheat stripe rust pathogen (Puccinia striiformis f. sp. tritici) and the barley stripe rust pathogen (Puccinia striiformis f. sp. hordei)

Genome sequence resources for the wheat stripe rust pathogen (Puccinia striiformis f. sp. tritici) and the barley stripe rust pathogen (Puccinia striiformis f. sp. hordei)

(2018) Chongjing Xia et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Inheritance of Virulence, Construction of a Linkage Map, and Mapping Dominant Virulence Genes in Puccinia striiformis f. sp. tritici Through Characterization of a Sexual Population with Genotyping-by-Sequencing

(2018) Congying Yuan et al.   PHYTOPATHOLOGY

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

Evolution and genome architecture in fungal plant pathogens

(2017) Mareike Möller et al.   NATURE REVIEWS MICROBIOLOGY

Virulence and Molecular Characterization of Experimental Isolates of the Stripe Rust Pathogen (Puccinia striiformis) Indicate Somatic Recombination

(2017) Yu Lei et al.   PHYTOPATHOLOGY

Changes of Races and Virulence Genes in Puccinia striiformis f. sp. tritici, the Wheat Stripe Rust Pathogen, in the United States from 1968 to 2009

(2017) Tinglan Liu et al.   PLANT DISEASE

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

Secretome Characterization and Correlation Analysis Reveal Putative Pathogenicity Mechanisms and Identify Candidate Avirulence Genes in the Wheat Stripe Rust Fungus Puccinia striiformis f. sp. tritici

(2017) Chongjing Xia et al.   Frontiers in Microbiology

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

(2017) Kanti Kiran et al.   Scientific Reports

Effector profiles distinguish formae speciales of Fusarium oxysporum

(2016) Peter van Dam et al.   ENVIRONMENTAL MICROBIOLOGY

Secreted protein gene derived-single nucleotide polymorphisms (SP-SNPs) reveal population diversity and differentiation of Puccinia striiformis f. sp. tritici in the United States

(2016) Chongjing Xia et al.   Fungal Biology

BlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences

(2016) Minoru Kanehisa et al.   JOURNAL OF MOLECULAR BIOLOGY

Hybridization of powdery mildew strains gives rise to pathogens on novel agricultural crop species

(2016) Fabrizio Menardo et al.   NATURE GENETICS

Evolution by gene loss

(2016) Ricard Albalat et al.   NATURE REVIEWS GENETICS

Grass Hosts Harbor More Diverse Isolates of Puccinia striiformis Than Cereal Crops

(2016) P. Cheng et al.   PHYTOPATHOLOGY

Races of Puccinia striiformis f. sp. tritici in the United States in 2011 and 2012 and Comparison with Races in 2010

(2016) Anmin Wan et al.   PLANT DISEASE

CASSIS and SMIPS: promoter-based prediction of secondary metabolite gene clusters in eukaryotic genomes

(2015) Thomas Wolf et al.   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

The two-speed genomes of filamentous pathogens: waltz with plants

(2015) Suomeng Dong et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Host specificity inSporisorium reilianumis determined by distinct mechanisms in maize and sorghum

(2015) Alana Poloni et al.   MOLECULAR PLANT PATHOLOGY

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Host jumps shaped the diversity of extant rust fungi (Pucciniales)

(2015) Alistair R. McTaggart et al.   NEW PHYTOLOGIST

The Transporter Classification Database (TCDB): recent advances

(2015) Milton H. Saier et al.   NUCLEIC ACIDS RESEARCH

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

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

Barberry as Alternate Host Is Important for Puccinia graminis f. sp. tritici But Not for Puccinia striiformis f. sp. tritici in the U.S. Pacific Northwest

(2015) M. N. Wang et al.   PLANT DISEASE

Barberry Does Not Function as an Alternate Host for Puccinia striiformis f. sp. tritici in the U. S. Pacific Northwest Due to Teliospore Degradation and Barberry Phenology

(2015) M. N. Wang et al.   PLANT DISEASE

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

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

proovread : large-scale high-accuracy PacBio correction through iterative short read consensus

(2014) Thomas Hackl et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Virulence and Molecular Analyses Support Asexual Reproduction of Puccinia striiformis f. sp. tritici in the U.S. Pacific Northwest

(2014) P. Cheng et al.   PHYTOPATHOLOGY

Virulence Characterization of Puccinia striiformis f. sp. tritici Using a New Set of Yr Single-Gene Line Differentials in the United States in 2010

(2014) Anmin Wan et al.   PLANT DISEASE

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

Formae specialesof cereal powdery mildew: close or distant relatives?

(2013) Veronique Troch et al.   MOLECULAR PLANT PATHOLOGY

The wheat powdery mildew genome shows the unique evolution of an obligate biotroph

(2013) Thomas Wicker et al.   NATURE GENETICS

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

(2013) Wenming Zheng et al.   Nature Communications

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

(2012) Pablo Cingolani et al.   FLY

Emerging fungal threats to animal, plant and ecosystem health

(2012) Matthew C. Fisher et al.   NATURE

Genome evolution in filamentous plant pathogens: why bigger can be better

(2012) Sylvain Raffaele et al.   NATURE REVIEWS MICROBIOLOGY

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

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

Genetic Variation inPuccinia graminisCollected from Oats, Rye, and Barberry

(2012) Anna Berlin et al.   PHYTOPATHOLOGY

Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution

(2012) K. E. Langergraber et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Diversity ofPuccinia striiformison Cereals and Grasses

(2011) Mogens S. Hovmøller et al.   Annual Review of Phytopathology

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

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

(2011) Mark A DePristo et al.   NATURE GENETICS

The evolutionary origin of orphan genes

(2011) Diethard Tautz et al.   NATURE REVIEWS GENETICS

Virulence, Frequency, and Distribution of Races of Puccinia striiformis f. sp. tritici and P. striiformis f. sp. hordei Identified in the United States in 2008 and 2009

(2011) Anmin Wan et al.   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

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

Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations

(2011) Thierry Rouxel et al.   Nature Communications

Multiple Translocation of the AVR-Pita Effector Gene among Chromosomes of the Rice Blast Fungus Magnaporthe oryzae and Related Species

(2011) Izumi Chuma et al.   PLoS Pathogens

An evolutionary review of human telomere biology: The thrifty telomere hypothesis and notes on potential adaptive paternal effects

(2010) Dan T.A. Eisenberg   AMERICAN JOURNAL OF HUMAN BIOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

(2010) Li-Jun Ma et al.   NATURE

Genome Expansion and Gene Loss in Powdery Mildew Fungi Reveal Tradeoffs in Extreme Parasitism

(2010) P. D. Spanu et al.   SCIENCE

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans

(2009) Brian J. Haas et al.   NATURE

The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion

(2009) Jeffrey J. Coleman et al.   PLoS Genetics

The Origins of Plant Pathogens in Agro-Ecosystems

(2008) Eva H. Stukenbrock et al.   Annual Review of Phytopathology

Characterization of Chromosome Ends in the Filamentous Fungus Neurospora crassa

(2008) C. Wu et al.   GENETICS

Acc homoeoloci and the evolution of wheat genomes

(2008) D. Chalupska et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA