Distinct Life Histories Impact Dikaryotic Genome Evolution in the Rust Fungus Puccinia striiformis Causing Stripe Rust in Wheat

Network-based microsynteny analysis identifies major differences and genomic outliers in mammalian and angiosperm genomes

(2019) Tao Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The global burden of pathogens and pests on major food crops

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

Genome Sequence Resource of a Puccinia striiformis Isolate infecting wheatgrass

(2019) Yuxiang Li et al.   PHYTOPATHOLOGY

Heterogeneous transposable elements as silencers, enhancers and targets of meiotic recombination

(2019) Charles J. Underwood et al.   CHROMOSOMA

Genomic signatures of heterokaryosis in the oomycete pathogen Bremia lactucae

(2019) Kyle Fletcher et al.   Nature Communications

MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens

(2019) Guru V. Radhakrishnan et al.   BMC BIOLOGY

Stress-driven transposable element de-repression dynamics and virulence evolution in a fungal pathogen

(2019) Simone Fouché et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Parauncinula polyspora Draft Genome Provides Insights into Patterns of Gene Erosion and Genome Expansion in Powdery Mildew Fungi

(2019) Lamprinos Frantzeskakis et al.   mBio

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

(2019) Feng Li et al.   Nature Communications

The complete mitochondrial genomes of Puccinia striiformis f. sp. tritici and Puccinia recondita f. sp. tritici

(2019) Chuang Li et al.   Mitochondrial DNA Part B-Resources

Signatures of host specialization and a recent transposable element burst in the dynamic one-speed genome of the fungal barley powdery mildew pathogen

(2018) Lamprinos Frantzeskakis et al.   BMC GENOMICS

Mt- rps 3 is an ancient gene which provides insight into the evolution of fungal mitochondrial genomes

(2018) Artemis G. Korovesi et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Improved prediction of fungal effector proteins from secretomes with EffectorP 2.0

(2018) Jana Sperschneider et al.   MOLECULAR PLANT PATHOLOGY

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

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)

(2018) Chongjing Xia et al.   BMC GENOMICS

Why outcross? The abandon-ship hypothesis in a facultative outcrossing/selfing fungal species

(2018) Océane Seudre et al.   FUNGAL GENETICS AND BIOLOGY

A New Reference Genome Shows the One-Speed Genome Structure of the Barley Pathogen Ramularia collo-cygni

(2018) Remco Stam et al.   Genome Biology and Evolution

The need for speed: compartmentalized genome evolution in filamentous phytopathogens

(2018) Lamprinos Frantzeskakis et al.   MOLECULAR PLANT PATHOLOGY

A chromosome-scale genome assembly reveals a highly dynamic effector repertoire of wheat powdery mildew

(2018) Marion C. Müller et al.   NEW PHYTOLOGIST

Advances in understanding obligate biotrophy in rust fungi

(2018) Cécile Lorrain et al.   NEW PHYTOLOGIST

Pathogenomic Analysis of Wheat Yellow Rust Lineages Detects Seasonal Variation and Host Specificity

(2017) Vanessa Bueno-Sancho et al.   Genome Biology and Evolution

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

(2017) Sergey Koren et al.   GENOME RESEARCH

GeSeq – versatile and accurate annotation of organelle genomes

(2017) Michael Tillich et al.   NUCLEIC ACIDS RESEARCH

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

(2017) Yu Lei et al.   PHYTOPATHOLOGY

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

Yellow Rust Epidemics Worldwide Were Caused by Pathogen Races from Divergent Genetic Lineages

(2017) Sajid Ali et al.   Frontiers in Plant Science

Tetrad analysis in plants and fungi finds large differences in gene conversion rates but no GC bias

(2017) Haoxuan Liu et al.   Nature Ecology & Evolution

Disease Impact on Wheat Yield Potential and Prospects of Genetic Control

(2016) Ravi P. Singh et al.   Annual Review of Phytopathology

Assemblytics: a web analytics tool for the detection of variants from an assembly

(2016) Maria Nattestad et al.   BIOINFORMATICS

The host-pathogen interaction between wheat and yellow rust induces temporally coordinated waves of gene expression

(2016) Albor Dobon et al.   BMC GENOMICS

Worldwide population structure of the wheat rust fungus Puccinia striiformis in the past

(2016) T. Thach et al.   FUNGAL GENETICS AND BIOLOGY

cloncase: Estimation of sex frequency and effective population size by clonemate resampling in partially clonal organisms

(2016) Sajid Ali et al.   Molecular Ecology Resources

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

(2016) Fabrizio Menardo et al.   NATURE GENETICS

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

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

Fundamental wheat stripe rust research in the 21st century

(2016) Benjamin Schwessinger   NEW PHYTOLOGIST

The Role of Hybridization in the Evolution and Emergence of New Fungal Plant Pathogens

(2016) Eva H. Stukenbrock   PHYTOPATHOLOGY

Evaluation of Spray and Point Inoculation Methods for the Phenotyping of Puccinia striiformis on Wheat

(2016) Chris K. Sørensen et al.   PLANT DISEASE

Molecular markers for tracking the origin and worldwide distribution of invasive strains ofPuccinia striiformis

(2016) Stephanie Walter et al.   Ecology and Evolution

Population genomics reveals the origin and asexual evolution of human infective trypanosomes

(2016) William Weir et al.   eLife

Recovery and virulence phenotyping of the historic ‘Stubbs collection’ of the yellow rust fungusPuccinia striiformisfrom wheat

(2015) T. Thach et al.   ANNALS OF APPLIED BIOLOGY

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

CodingQuarry: highly accurate hidden Markov model gene prediction in fungal genomes using RNA-seq transcripts

(2015) Alison C Testa et al.   BMC GENOMICS

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

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Effector P: predicting fungal effector proteins from secretomes using machine learning

(2015) Jana Sperschneider et al.   NEW PHYTOLOGIST

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas 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

Replacement of the European wheat yellow rust population by new races from the centre of diversity in the near-Himalayan region

(2015) M. S. Hovmøller et al.   PLANT PATHOLOGY

Clonal reproduction in fungi

(2015) John W. Taylor et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Field pathogenomics reveals the emergence of a diverse wheat yellow rust population

(2015) Amelia Hubbard et al.   GENOME BIOLOGY

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Evolution of sexual reproduction: A view from the fungal kingdom supports an evolutionary epoch with sex before sexes

(2015) Joseph Heitman   Fungal Biology Reviews

Research investment implications of shifts in the global geography of wheat stripe rust

(2015) Jason M. Beddow et al.   Nature Plants

Computel: Computation of Mean Telomere Length from Whole-Genome Next-Generation Sequencing Data

(2015) Lilit Nersisyan et al.   PLoS One

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

Mobile elements and mitochondrial genome expansion in the soil fungus and potato pathogenRhizoctonia solaniAG-3

(2014) Liliana Losada et al.   FEMS MICROBIOLOGY LETTERS

Sexual structures and recombination of the wheat rust fungus Puccinia striiformis on Berberis vulgaris

(2014) Julian Rodriguez-Algaba et al.   FUNGAL GENETICS AND BIOLOGY

High Variability of Mitochondrial Gene Order among Fungi

(2014) Gabriela Aguileta et al.   Genome Biology and Evolution

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

New Races of Puccinia striiformis Found in Europe Reveal Race Specificity of Long-Term Effective Adult Plant Resistance in Wheat

(2014) Chris K. Sørensen et al.   PHYTOPATHOLOGY

Novel Telomere-Anchored PCR Approach for Studying Sexual Stage Telomeres in Aspergillus nidulans

(2014) Nengding Wang et al.   PLoS One

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

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

Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana

(2014) Florian Maumus et al.   Nature Communications

Origin, Migration Routes and Worldwide Population Genetic Structure of the Wheat Yellow Rust Pathogen Puccinia striiformis f.sp. tritici

(2014) Sajid Ali et al.   PLoS Pathogens

The past, present and future of breeding rust resistant wheat

(2014) Jeffrey G. Ellis et al.   Frontiers in Plant Science

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

Comparative analysis of mitochondrial genomes from closely related Rhynchosporium species reveals extensive intron invasion

(2013) Stefano F.F. Torriani et al.   FUNGAL GENETICS AND BIOLOGY

Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes

(2013) Pierre Gladieux et al.   MOLECULAR ECOLOGY

Wheat stripe (yellow) rust caused byPuccinia striiformisf. sp.tritici

(2013) Wanquan Chen et al.   MOLECULAR PLANT PATHOLOGY

MycoCosm portal: gearing up for 1000 fungal genomes

(2013) Igor V. Grigoriev 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

MITOS: Improved de novo metazoan mitochondrial genome annotation

(2012) Matthias Bernt et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Somatic Hybridization in the Uredinales

(2011) Robert F. Park et al.   Annual Review of Phytopathology

Pybedtools: a flexible Python library for manipulating genomic datasets and annotations

(2011) Ryan K. Dale et al.   BIOINFORMATICS

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

(2011) Guillaume Marçais et al.   BIOINFORMATICS

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

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

Global status of stripe rust: a review of historical and current threats

(2011) Colin R. Wellings   EUPHYTICA

Genetic structure and local adaptation of European wheat yellow rust populations: the role of temperature-specific adaptation

(2011) Mamadou Mboup et al.   Evolutionary Applications

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

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

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Puccinia striiformis f.sp. tritici presents high diversity and recombination in the over-summering zone of Gansu, China

(2010) X. Duan et al.   MYCOLOGIA

Analysis of the complete mitochondrial genome sequences of the soybean rust pathogens Phakopsora pachyrhizi and P. meibomiae

(2010) Christine L. Stone et al.   MYCOLOGIA

Century-Old Mystery of Puccinia striiformis Life History Solved with the Identification of Berberis as an Alternate Host

(2010) Yue Jin et al.   PHYTOPATHOLOGY

The role of sex in fungal evolution

(2009) Clifford Zeyl   CURRENT OPINION IN MICROBIOLOGY

Rapid global spread of two aggressive strains of a wheat rust fungus

(2008) MOGENS S. HOVMØLLER et al.   MOLECULAR ECOLOGY

Telomeres and Aging

(2008) Geraldine Aubert et al.   PHYSIOLOGICAL REVIEWS

Emergence of a Novel Population of Puccinia striiformis f. sp. tritici in Eastern United States

(2008) S. G. Markell et al.   PHYTOPATHOLOGY

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

(2008) Brian J Haas et al.   GENOME BIOLOGY