Haplotype‐phased and chromosome‐level genome assembly of Puccinia polysora , a giga‐scale fungal pathogen causing southern corn rust

The RppC-AvrRppC NLR-effector Interaction Mediates the Resistance to Southern Corn Rust in Maize

(2022) Ce Deng et al.   Molecular Plant

TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes

(2022) Ren-Gang Zhang et al.   Horticulture Research

Duplex Telomere-Binding Proteins in Fungi With Canonical Telomere Repeats: New Lessons in the Rapid Evolution of Telomere Proteins

(2021) Neal F. Lue   Frontiers in Genetics

Molecular Characterization of Wheat Stripe Rust Pathogen (Puccinia striiformis f. sp. tritici) Collections from Nine Countries

(2021) Qing Bai et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes

(2021) Mosè Manni et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Chromosome-Scale Assembly of the Wheat Leaf Rust Pathogen Puccinia triticina Provides Insights Into Structural Variations and Genetic Relationships With Haplotype Resolution

(2021) Jing Qin Wu et al.   Frontiers in Microbiology

EffectorP 3.0: Prediction of Apoplastic and Cytoplasmic Effectors in Fungi and Oomycetes

(2021) Jana Sperschneider et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Evolution of virulence in rust fungi — multiple solutions to one problem

(2020) Melania Figueroa et al.   CURRENT OPINION IN PLANT BIOLOGY

HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads

(2020) Sergey Nurk et al.   GENOME RESEARCH

Gymnosporangium species on Malus: species delineation, diversity and host alternation

(2020) P. Zhao et al.   PERSOONIA

Increased virulence of Puccinia coronata f. sp.avenae populations through allele frequency changes at multiple putative Avr loci

(2020) Marisa E. Miller et al.   PLoS Genetics

Rapid evolution in plant–microbe interactions – a molecular genomics perspective

(2019) Lamprinos Frantzeskakis et al.   NEW PHYTOLOGIST

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

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

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

Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization

(2018) Joachim Wolff et al.   NUCLEIC ACIDS RESEARCH

Deconstructing the evolutionary complexity between rust fungi ( Pucciniales ) and their plant hosts

(2018) M.C. Aime et al.   STUDIES IN MYCOLOGY

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

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

Austropuccinia psidii on the move: survey based insights to its geographical distribution, host species, impacts and management in Australia

(2018) Laura Fernandez Winzer et al.   BIOLOGICAL INVASIONS

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

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

De novo assembly of haplotype-resolved genomes with trio binning

(2018) Sergey Koren et al.   NATURE BIOTECHNOLOGY

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Global risk levels for corn rusts (Puccinia sorghi and Puccinia polysora ) under climate change projections

(2017) Nadiezhda Yakovleva Zitz Ramirez-Cabral et al.   JOURNAL OF PHYTOPATHOLOGY

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

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

Genome expansion and lineage-specific genetic innovations in the forest pathogenic fungi Armillaria

(2017) György Sipos et al.   Nature Ecology & Evolution

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

vcfr: a package to manipulate and visualize variant call format data in R

(2016) Brian J. Knaus et al.   Molecular Ecology Resources

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

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

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

The Hemileia vastatrix effector HvEC-016 suppresses bacterial blight symptoms in coffee genotypes with the S H 1 rust resistance gene

(2016) Thiago Maia et al.   NEW PHYTOLOGIST

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

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

Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles

(2016) Raúl Castanera et al.   PLoS Genetics

Changing the Game: Using Integrative Genomics to Probe Virulence Mechanisms of the Stem Rust Pathogen Puccinia graminis f. sp. tritici

(2016) Melania Figueroa et al.   Frontiers in Plant Science

Effector-Triggered Immunity: From Pathogen Perception to Robust Defense

(2015) Haitao Cui et al.   Annual Review of Plant Biology

Fungal Effectors and Plant Susceptibility

(2015) Libera Lo Presti et al.   Annual Review of Plant Biology

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Extraordinary Genetic Diversity in a Wood Decay Mushroom

(2015) Maria A. Baranova et al.   MOLECULAR BIOLOGY AND EVOLUTION

Flow cytometry reveals that the rust fungus,Uromyces bidentis(Pucciniales), possesses the largest fungal genome reported-2489 Mbp

(2015) Ana Paula Ramos et al.   MOLECULAR PLANT PATHOLOGY

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

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

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R

(2014) Bastian Pfeifer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Poppr: an R package for genetic analysis of populations with clonal, partially clonal, and/or sexual reproduction

(2014) Zhian N. Kamvar et al.   PeerJ

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

(2013) Y. Liao et al.   BIOINFORMATICS

Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen

(2013) R. de Jonge et al.   GENOME RESEARCH

Pfam: the protein families database

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

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

(2012) Pablo Cingolani et al.   FLY

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

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

Transposable elements and viruses as factors in adaptation and evolution: an expansion and strengthening of the TE-Thrust hypothesis

(2012) Keith R. Oliver et al.   Ecology and Evolution

The Emergence of Ug99 Races of the Stem Rust Fungus is a Threat to World Wheat Production

(2011) Ravi P. Singh et al.   Annual Review of Phytopathology

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

(2011) Guillaume Marçais et al.   BIOINFORMATICS

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

Real-Time PCR Detection and Discrimination of the Southern and Common Corn Rust Pathogens Puccinia polysora and Puccinia sorghi

(2011) Jo Anne Crouch et al.   PLANT DISEASE

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

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

(2010) Heng Li et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

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

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

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

(2010) Yue Jin et al.   PHYTOPATHOLOGY

Genetic signals of origin, spread, and introgression in a large sample of maize landraces

(2010) J. van Heerwaarden et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) P. D. Spanu et al.   SCIENCE

Transposable elements and an epigenetic basis for punctuated equilibria

(2009) David W. Zeh et al.   BIOESSAYS

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

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

(2008) Brian J Haas et al.   GENOME BIOLOGY