Genome assembly and characterization of a complex zfBED-NLR gene-containing disease resistance locus in Carolina Gold Select rice with Nanopore sequencing

The complex architecture and epigenomic impact of plant T-DNA insertions

(2019) Florian Jupe et al.   PLoS Genetics

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

(2019) Sanu Arora et al.   NATURE BIOTECHNOLOGY

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

(2018) Joshua C. Stein et al.   NATURE GENETICS

Piercing the dark matter: bioinformatics of long-range sequencing and mapping

(2018) Fritz J. Sedlazeck et al.   NATURE REVIEWS GENETICS

High contiguity Arabidopsis thaliana genome assembly with a single nanopore flow cell

(2018) Todd P. Michael et al.   Nature Communications

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

Hybrid assembly of the large and highly repetitive genome ofAegilops tauschii, a progenitor of bread wheat, with the MaSuRCA mega-reads algorithm

(2017) Aleksey V. Zimin et al.   GENOME RESEARCH

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species

(2017) Paul Julian Kersey et al.   NUCLEIC ACIDS RESEARCH

De Novo Assembly of a NewSolanum pennelliiAccession Using Nanopore Sequencing

(2017) Maximilian H.-W. Schmidt et al.   PLANT CELL

The first near-complete assembly of the hexaploid bread wheat genome, Triticum aestivum

(2017) Aleksey V Zimin et al.   GigaScience

Targeted capture and sequencing of gene-sized DNA molecules

(2016) Michael Giolai et al.   BIOTECHNIQUES

Comparative analysis of plant immune receptor architectures uncovers host proteins likely targeted by pathogens

(2016) Panagiotis F. Sarris et al.   BMC BIOLOGY

Pooled Enrichment Sequencing Identifies Diversity and Evolutionary Pressures at NLR Resistance Genes within a Wild Tomato Population

(2016) Remco Stam et al.   Genome Biology and Evolution

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

(2016) Burkhard Steuernagel et al.   NATURE BIOTECHNOLOGY

Accelerated cloning of a potato late blight–resistance gene using RenSeq and SMRT sequencing

(2016) Kamil Witek et al.   NATURE BIOTECHNOLOGY

Domestication history and geographical adaptation inferred from a SNP map of African rice

(2016) Rachel S Meyer et al.   NATURE GENETICS

Integration of decoy domains derived from protein targets of pathogen effectors into plant immune receptors is widespread

(2016) Thomas Kroj et al.   NEW PHYTOLOGIST

CDD/SPARCLE: functional classification of proteins via subfamily domain architectures

(2016) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

(2016) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

A resistance locus in the American heirloom rice variety Carolina Gold Select is triggered by TAL effectors with diverse predicted targets and is effective against African strains ofXanthomonas oryzaepv.oryzicola

(2016) Lindsay R. Triplett et al.   PLANT JOURNAL

Interfering TAL effectors of Xanthomonas oryzae neutralize R-gene-mediated plant disease resistance

(2016) Zhiyuan Ji et al.   Nature Communications

NLR-parser: rapid annotation of plant NLR complements

(2015) Burkhard Steuernagel et al.   BIOINFORMATICS

A Receptor Pair with an Integrated Decoy Converts Pathogen Disabling of Transcription Factors to Immunity

(2015) Clémentine Le Roux et al.   CELL

Whole Genome Sequencing of Elite Rice Cultivars as a Comprehensive Information Resource for Marker Assisted Selection

(2015) Jorge Duitama et al.   PLoS One

TAL effectors and activation of predicted host targets distinguish Asian from African strains of the rice pathogen Xanthomonas oryzae pv. oryzicola while strict conservation suggests universal importance of five TAL effectors

(2015) Katherine E. Wilkins et al.   Frontiers in Plant Science

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Defining the full tomato NB-LRR resistance gene repertoire using genomic and cDNA RenSeq

(2014) Giuseppe Andolfo et al.   BMC PLANT BIOLOGY

The NB‐LRR proteins RGA4 and RGA5 interact functionally and physically to confer disease resistance

(2014) Stella Césari et al.   EMBO JOURNAL

Rice blast resistance gene Pikahei-1(t), a member of a resistance gene cluster on chromosome 4, encodes a nucleotide-binding site and leucine-rich repeat protein

(2014) Xin Xu et al.   MOLECULAR BREEDING

The genome sequence of African rice (Oryza glaberrima) and evidence for independent domestication

(2014) Muhua Wang et al.   NATURE GENETICS

Close linkage of a blast resistance gene, Pias(t), with a bacterial leaf blight resistance gene, Xa1-as(t), in a rice cultivar ‘Asominori’

(2013) Takashi Endo et al.   BREEDING SCIENCE

Presence–Absence Variation in A. thaliana Is Primarily Associated with Genomic Signatures Consistent with Relaxed Selective Constraints

(2013) Stephen J. Bush et al.   MOLECULAR BIOLOGY AND EVOLUTION

Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations

(2013) Florian Jupe et al.   PLANT JOURNAL

Whole-genome sequencing of Oryza brachyantha reveals mechanisms underlying Oryza genome evolution

(2013) Jinfeng Chen et al.   Nature Communications

Evolution and Conservation of Plant NLR Functions

(2013) Florence Jacob et al.   Frontiers in Immunology

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

Detection of copy number variations in rice using array-based comparative genomic hybridization

(2011) Ping Yu et al.   BMC GENOMICS

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor)

(2011) Lei-Ying Zheng et al.   GENOME BIOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

TAL effectors: finding plant genes for disease and defense

(2010) Adam J Bogdanove et al.   CURRENT OPINION IN PLANT BIOLOGY

Unique evolutionary pattern of numbers of gramineous NBS–LRR genes

(2010) Jing Li et al.   MOLECULAR GENETICS AND GENOMICS

Innate immunity: has poplar made its BED?

(2010) Hugo Germain et al.   NEW PHYTOLOGIST

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Maintenance of genetic variation in plants and pathogens involves complex networks of gene-for-gene interactions

(2009) SHARON A. HALL et al.   MOLECULAR PLANT PATHOLOGY

Identification and fine mapping of the new bacterial blight resistance gene, Xa31(t), in rice

(2008) Chuntai Wang et al.   EUROPEAN JOURNAL OF PLANT PATHOLOGY

A novel bacterial blight resistance gene from Oryza nivara mapped to 38 kb region on chromosome 4L and transferred to Oryza sativa L.

(2008) KULJIT K. CHEEMA et al.   Genetics Research

Sequencing of natural strains of Arabidopsis thaliana with short reads

(2008) S. Ossowski et al.   GENOME RESEARCH

Structure–function analysis of the NB-ARC domain of plant disease resistance proteins

(2008) Gerben van Ooijen et al.   JOURNAL OF EXPERIMENTAL BOTANY

Independent Losses of Function in a Polyphenol Oxidase in Rice: Differentiation in Grain Discoloration between Subspecies and the Role of Positive Selection under Domestication

(2008) Y. Yu et al.   PLANT CELL

Fine mapping of a strong QTL of field resistance against rice blast, Pikahei-1(t), from upland rice Kahei, utilizing a novel resistance evaluation system in the greenhouse

(2008) Xin Xu et al.   THEORETICAL AND APPLIED GENETICS