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

Evolution within the fungal genus Verticillium is characterized by chromosomal rearrangement and gene loss

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Characterization and comparative analysis of the genome of Puccinia sorghi Schwein, the causal agent of maize common rust

(2018) Lucia Rochi et al.   FUNGAL GENETICS AND BIOLOGY

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

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

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The coffee leaf rust pathogen Hemileia vastatrix : one and a half centuries around the tropics

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A Puccinia striiformis f. sp. tritici secreted protein activates plant immunity at the cell surface

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An overview of genetic rust resistance: From broad to specific mechanisms

(2017) Sambasivam Periyannan et al.   PLoS Pathogens

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

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

Stop neglecting fungi

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Role of Alternate Hosts in Epidemiology and Pathogen Variation of Cereal Rusts

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

(2016) Albor Dobon et al.   BMC GENOMICS

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

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

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A Tale of Genome Compartmentalization: The Evolution of Virulence Clusters in Smut Fungi

(2016) Julien Y. Dutheil et al.   Genome Biology and Evolution

Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen

(2016) Luigi Faino et al.   GENOME RESEARCH

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

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

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The stripe rust fungal effector PEC6 suppresses pattern-triggered immunity in a host species-independent manner and interacts with adenosine kinases

(2016) Changhai Liu et al.   NEW PHYTOLOGIST

Fundamental wheat stripe rust research in the 21st century

(2016) Benjamin Schwessinger   NEW PHYTOLOGIST

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The Evolution of Orphan Regions in Genomes of a Fungal Pathogen of Wheat

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

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Leaf Rust of Cultivated Barley: Pathology and Control

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

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

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

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PacBio-LITS: a large-insert targeted sequencing method for characterization of human disease-associated chromosomal structural variations

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

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

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

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

CRN13 candidate effectors from plant and animal eukaryotic pathogens are DNA-binding proteins which trigger host DNA damage response

(2015) Diana Ramirez-Garcés et al.   NEW PHYTOLOGIST

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

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

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Ensembl Genomes 2016: more genomes, more complexity

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

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

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Single-Molecule Real-Time Sequencing Combined with Optical Mapping Yields Completely Finished Fungal Genome

(2015) Luigi Faino et al.   mBio

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

(2015) Jana Sperschneider et al.   PLoS Pathogens

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

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

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InterProScan 5: genome-scale protein function classification

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

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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

Effector proteins of rust fungi

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

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

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

The past, present and future of breeding rust resistant wheat

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featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

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Genome analyses of the wheat yellow (stripe) rust pathogen Puccinia striiformis f. sp. tritici reveal polymorphic and haustorial expressed secreted proteins as candidate effectors

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Inferring the contribution of sexual reproduction, migration and off-season survival to the temporal maintenance of microbial populations: a case study on the wheat fungal pathogenPuccinia striiformisf.sp.tritici

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

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MycoCosm portal: gearing up for 1000 fungal genomes

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Identification of Eighteen Berberis Species as Alternate Hosts of Puccinia striiformis f. sp. tritici and Virulence Variation in the Pathogen Isolates from Natural Infection of Barberry Plants in China

(2013) Jie Zhao et al.   PHYTOPATHOLOGY

Strategies for Wheat Stripe Rust Pathogenicity Identified by Transcriptome Sequencing

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

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The Top 10 fungal pathogens in molecular plant pathology

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

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The Irish Potato Famine Pathogen Phytophthora infestans Translocates the CRN8 Kinase into Host Plant Cells

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Diversity ofPuccinia striiformison Cereals and Grasses

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The NumPy Array: A Structure for Efficient Numerical Computation

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

(2011) Colin R. Wellings   EUPHYTICA

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Considering Transposable Element Diversification in De Novo Annotation Approaches

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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

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Finished Genome of the Fungal Wheat Pathogen Mycosphaerella graminicola Reveals Dispensome Structure, Chromosome Plasticity, and Stealth Pathogenesis

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Reduction in the sex ability of worldwide clonal populations of Puccinia striiformis f.sp. tritici

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Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

(2010) Li-Jun Ma et al.   NATURE

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

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Dating the molecular clock in fungi – how close are we?

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Breeding cereals for rust resistance in Australia

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