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

Whole-genome sequencing of Puccinia striiformis f. sp. tritici mutant isolates identifies avirulence gene candidates

(2020) Yuxiang Li et al.   BMC GENOMICS

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

(2020) Benjamin Schwessinger et al.   Genome Biology and Evolution

Pan-Genome of Wild and Cultivated Soybeans

(2020) Yucheng Liu et al.   CELL

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

Integrated Analysis of Gene Expression, SNP, InDel, and CNV Identifies Candidate Avirulence Genes in Australian Isolates of the Wheat Leaf Rust Pathogen Puccinia triticina

(2020) Long Song et al.   Genes

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

Rust pathogen effectors: perspectives in resistance breeding

(2019) Pramod Prasad et al.   PLANTA

Genotyping-by-Sequencing for the Study of Genetic Diversity in Puccinia triticina

(2019) Meriem Aoun et al.   PLANT DISEASE

Pangenomics Comes of Age: From Bacteria to Plant and Animal Applications

(2019) Agnieszka A. Golicz et al.   TRENDS IN GENETICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

De Novo Assembly and Phasing of Dikaryotic Genomes from Two Isolates of Puccinia coronata f. sp. avenae, the Causal Agent of Oat Crown Rust

(2018) Marisa E. Miller et al.   mBio

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

An Overview of the Function and Maintenance of Sexual Reproduction in Dikaryotic Fungi

(2018) R. M. Wallen et al.   Frontiers in Microbiology

Two Methods for Mapping and Visualizing Associated Data on Phylogeny Using Ggtree

(2018) Guangchuang Yu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly of the domestic goat genome

(2017) Derek M Bickhart et al.   NATURE GENETICS

Loss ofAvrSr50by somatic exchange in stem rust leads to virulence forSr50resistance in wheat

(2017) Jiapeng Chen et al.   SCIENCE

Comparative Genomics Integrated with Association Analysis Identifies Candidate Effector Genes Corresponding to Lr20 in Phenotype-Paired Puccinia triticina Isolates from Australia

(2017) Jing Qin Wu et al.   Frontiers in Plant Science

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

(2016) Maria Nattestad et al.   BIOINFORMATICS

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

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

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

(2016) Mihaela Pertea et al.   Nature Protocols

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

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

Physiologic Specialization of Puccinia triticina on Wheat in the United States in 2014

(2016) J. A. Kolmer et al.   PLANT DISEASE

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

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

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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

Evolution of Mating Systems in Basidiomycetes and the Genetic Architecture Underlying Mating-Type Determination in the Yeast Leucosporidium scottii

(2015) T. M. Maia et al.   GENETICS

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

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

SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data

(2014) Tae-Ho Lee et al.   BMC GENOMICS

Evolution of uni- and bifactorial sexual compatibility systems in fungi

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Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

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

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

(2012) Yanbin Yin et al.   NUCLEIC ACIDS RESEARCH

Discovery of a Modified Tetrapolar Sexual Cycle in Cryptococcus amylolentus and the Evolution of MAT in the Cryptococcus Species Complex

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Somatic Hybridization in the Uredinales

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

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Gene discovery in EST sequences from the wheat leaf rust fungus Puccinia triticina sexual spores, asexual spores and haustoria, compared to other rust and corn smut fungi

(2011) Junhuan Xu et al.   BMC GENOMICS

Global status of wheat leaf rust caused by Puccinia triticina

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The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

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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