Long-read genome sequencing of bread wheat facilitates disease resistance gene cloning

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

(2021) Haoyu Cheng et al.   NATURE METHODS

A membrane-bound ankyrin repeat protein confers race-specific leaf rust disease resistance in wheat

(2021) Markus C. Kolodziej et al.   Nature Communications

Creation and judicious application of a wheat resistance gene atlas

(2021) Amber N. Hafeez et al.   Molecular Plant

High-temperature wheat leaf rust resistance gene exhibits pleiotropic effects on hybrid necrosis

(2021) Xiaocui Yan et al.   Molecular Plant

Wheat leaf rust resistance gene Lr13 is a specific Ne2 allele for hybrid necrosis

(2021) Timothy Hewitt et al.   Molecular Plant

Optical maps refine the bread wheat Triticum aestivum cv. Chinese Spring genome assembly

(2021) Tingting Zhu et al.   PLANT JOURNAL

Population genomics and haplotype analysis in spelt and bread wheat identifies a gene regulating glume color

(2021) Michael Abrouk et al.   Communications Biology

The NLR-Annotator tool enables annotation of the intracellular immune receptor repertoire

(2020) Burkhard Steuernagel et al.   PLANT PHYSIOLOGY

LRRpredictor—A New LRR Motif Detection Method for Irregular Motifs of Plant NLR Proteins Using an Ensemble of Classifiers

(2020) Eliza C. Martin et al.   Genes

Chromosome-Scale Assembly of the Bread Wheat Genome Reveals Thousands of Additional Gene Copies

(2020) Michael Alonge et al.   GENETICS

UCSF ChimeraX : Structure visualization for researchers, educators, and developers

(2020) Eric F. Pettersen et al.   PROTEIN SCIENCE

Multiple wheat genomes reveal global variation in modern breeding

(2020) Sean Walkowiak et al.   NATURE

Direct pathogen-induced assembly of an NLR immune receptor complex to form a holoenzyme

(2020) Shoucai Ma et al.   SCIENCE

Phenotyping Kariega × Avocet S doubled haploid lines containing individual and combined adult plant stripe rust resistance loci

(2019) G. J. Maree et al.   PLANT PATHOLOGY

Resistance gene cloning from a wild crop relative by sequence capture and association genetics

(2019) Sanu Arora et al.   NATURE BIOTECHNOLOGY

Durum wheat genome highlights past domestication signatures and future improvement targets

(2019) Marco Maccaferri et al.   NATURE GENETICS

Reconstitution and structure of a plant NLR resistosome conferring immunity

(2019) Jizong Wang et al.   SCIENCE

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

(2019) Aaron M. Wenger et al.   NATURE BIOTECHNOLOGY

First Report of Puccinia striiformis f. sp. tritici, Causing Stripe Rust of Wheat, in Zimbabwe

(2019) Willem H.P. Boshoff et al.   PLANT DISEASE

siRNA-Finder (si-Fi) Software for RNAi-Target Design and Off-Target Prediction

(2019) Stefanie Lück et al.   Frontiers in Plant Science

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Defended to the Nines: 25 Years of Resistance Gene Cloning Identifies Nine Mechanisms for R Protein Function

(2018) Jiorgos Kourelis et al.   PLANT CELL

Pyramiding of transgenic Pm3 alleles in wheat results in improved powdery mildew resistance in the field

(2018) Teresa Koller et al.   THEORETICAL AND APPLIED GENETICS

A fast adaptive algorithm for computing whole-genome homology maps

(2018) Chirag Jain et al.   BIOINFORMATICS

Shifting the limits in wheat research and breeding using a fully annotated reference genome

(2018) et al.   SCIENCE

Rapid cloning of genes in hexaploid wheat using cultivar-specific long-range chromosome assembly

(2017) Anupriya Kaur Thind et al.   NATURE BIOTECHNOLOGY

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

Wild emmer genome architecture and diversity elucidate wheat evolution and domestication

(2017) Raz Avni 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

Extraction of high-molecular-weight genomic DNA for long-read sequencing of single molecules

(2016) Baptiste Mayjonade et al.   BIOTECHNIQUES

Rapid cloning of disease-resistance genes in plants using mutagenesis and sequence capture

(2016) Burkhard Steuernagel et al.   NATURE BIOTECHNOLOGY

Characterization of a Wheat Breeders’ Array suitable for high-throughput SNP genotyping of global accessions of hexaploid bread wheat (Triticum aestivum)

(2016) Alexandra M. Allen et al.   PLANT BIOTECHNOLOGY JOURNAL

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

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

(2016) Neva C. Durand et al.   Cell Systems

Virus induced gene silencing (VIGS) for functional analysis of wheat genes involved in Zymoseptoria tritici susceptibility and resistance

(2015) Wing-Sham Lee et al.   FUNGAL GENETICS AND BIOLOGY

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

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

The Phyre2 web portal for protein modeling, prediction and analysis

(2015) Lawrence A Kelley et al.   Nature Protocols

The MEME Suite

(2015) Timothy L. Bailey et al.   NUCLEIC ACIDS RESEARCH

High-resolution mapping and new marker development for adult plant stripe rust resistance QTL in the wheat cultivar Kariega

(2014) G. M. Agenbag et al.   MOLECULAR BREEDING

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

RNA-Seq bulked segregant analysis enables the identification of high-resolution genetic markers for breeding in hexaploid wheat

(2014) Ricardo H. Ramirez-Gonzalez et al.   PLANT BIOTECHNOLOGY JOURNAL

Characterization of polyploid wheat genomic diversity using a high-density 90 000 single nucleotide polymorphism array

(2014) Shichen Wang et al.   PLANT BIOTECHNOLOGY JOURNAL

The Gene Sr33, an Ortholog of Barley Mla Genes, Encodes Resistance to Wheat Stem Rust Race Ug99

(2013) S. Periyannan et al.   SCIENCE

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Identification and localisation of the NB-LRR gene family within the potato genome

(2012) Florian Jupe et al.   BMC GENOMICS

A High Throughput Barley Stripe Mosaic Virus Vector for Virus Induced Gene Silencing in Monocots and Dicots

(2011) Cheng Yuan et al.   PLoS One

The wheat Mla homologue TmMla1 exhibits an evolutionarily conserved function against powdery mildew in both wheat and barley

(2010) Tina Jordan et al.   PLANT JOURNAL

A Putative ABC Transporter Confers Durable Resistance to Multiple Fungal Pathogens in Wheat

(2009) S. G. Krattinger et al.   SCIENCE