Nuclear exchange generates population diversity in the wheat leaf rust pathogen Puccinia triticina

Haplotype-resolved assembly of diploid genomes without parental data

(2022) Haoyu Cheng et al.   NATURE BIOTECHNOLOGY

Sexual reproduction is the null hypothesis for life cycles of rust fungi

(2022) Alistair R. McTaggart et al.   PLoS Pathogens

Wheat Stem Rust Back in Europe: Diversity, Prevalence and Impact on Host Resistance

(2022) Mehran Patpour et al.   Frontiers in Plant Science

A chromosome-level, fully phased genome assembly of the oat crown rust fungus Puccinia coronata f. sp. avenae: a resource to enable comparative genomics in the cereal rusts

(2022) Eva C Henningsen et al.   G3-Genes Genomes Genetics

Population genomics of Puccinia graminis f.sp. tritici highlights the role of admixture in the origin of virulent wheat rust races

(2022) Yuanwen Guo et al.   Nature Communications

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C

(2021) Zev N. Kronenberg et al.   Nature Communications

Whole-genome sequencing of multiple isolates of Puccinia triticina reveals asexual lineages evolving by recurrent mutations

(2021) John P Fellers et al.   G3-Genes Genomes Genetics

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

IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era

(2020) Bui Quang Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

RepeatModeler2 for automated genomic discovery of transposable element families

(2020) Jullien M. Flynn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

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

(2020) Jing Qin Wu et al.   Frontiers in Genetics

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

(2020) Sergey Nurk et al.   GENOME RESEARCH

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

Virulence of Puccinia triticina, the wheat leaf rust fungus, in the United States in 2017.

(2019) James Kolmer   PLANT DISEASE

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Integrating Hi-C links with assembly graphs for chromosome-scale assembly

(2019) Jay Ghurye et al.   PLoS Computational Biology

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

(2019) Feng Li et al.   Nature Communications

Endemic and panglobal genetic groups, and divergence of host-associated forms in worldwide collections of the wheat leaf rust fungus Puccinia triticina as determined by genotyping by sequencing

(2019) J. A. Kolmer et al.   HEREDITY

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

High-resolution TADs reveal DNA sequences underlying genome organization in flies

(2018) Fidel Ramírez et al.   Nature Communications

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

D-GENIES: dot plot large genomes in an interactive, efficient and simple way

(2018) Floréal Cabanettes et al.   PeerJ

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

(2017) Sergey Koren et al.   GENOME RESEARCH

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

(2017) Eric S. Nazareno et al.   MOLECULAR PLANT PATHOLOGY

A review of wheat diseases-a field perspective

(2017) Melania Figueroa et al.   MOLECULAR PLANT PATHOLOGY

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

(2017) Yu Lei et al.   PHYTOPATHOLOGY

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

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

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

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2012) Pablo Cingolani et al.   FLY

Genetic differentiation of the wheat leaf rust fungusPuccinia triticinain Europe

(2012) J. A. Kolmer et al.   PLANT PATHOLOGY

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Global status of wheat leaf rust caused by Puccinia triticina

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

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

Genetic Differentiation Within the Puccinia triticina Population in South America and Comparison with the North American Population Suggests Common Ancestry and Intercontinental Migration

(2010) M. E. Ordoñez et al.   PHYTOPATHOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Differentiation of Molecular Genotypes and Virulence Phenotypes ofPuccinia triticinafrom Common Wheat in North America

(2009) M. E. Ordoñez et al.   PHYTOPATHOLOGY

Occurrence of wheat leaf rust (Puccinia triticina) races and virulence changes in Slovakia in 1994–2004

(2008) Alena Hanzalová et al.   BIOLOGIA

Wheat leaf rust caused byPuccinia triticina

(2008) MELVIN D. BOLTON et al.   MOLECULAR PLANT PATHOLOGY

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

(2008) Brian J Haas et al.   GENOME BIOLOGY