Small RNA discovery in the interaction between barley and the powdery mildew pathogen

Signatures of host specialization and a recent transposable element burst in the dynamic one-speed genome of the fungal barley powdery mildew pathogen

(2018) Lamprinos Frantzeskakis et al.   BMC GENOMICS

Identification of cold stress responsive microRNAs in two winter turnip rape (Brassica rapa L.) by high throughput sequencing

(2018) Xiucun Zeng et al.   BMC PLANT BIOLOGY

Cereal powdery mildew effectors: a complex toolbox for an obligate pathogen

(2018) Salim Bourras et al.   CURRENT OPINION IN MICROBIOLOGY

Transient Overexpression of HvSERK2 Improves Barley Resistance to Powdery Mildew

(2018) Yingbo Li et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

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

(2018) Jiorgos Kourelis et al.   PLANT CELL

Knockdown of Rice MicroRNA166 Confers Drought Resistance by Causing Leaf Rolling and Altering Stem Xylem Development

(2018) Jinshan Zhang et al.   PLANT PHYSIOLOGY

Small RNAs from cereal powdery mildew pathogens may target host plant genes

(2018) Stefan Kusch et al.   Fungal Biology

Glutamate synthase MoGlt1-mediated glutamate homeostasis is important for autophagy, virulence and conidiation in the rice blast fungus

(2017) Wei Zhou et al.   MOLECULAR PLANT PATHOLOGY

A chromosome conformation capture ordered sequence of the barley genome

(2017) Martin Mascher et al.   NATURE

The Emergence, Evolution, and Diversification of the miR390-TAS3-ARF Pathway in Land Plants

(2017) Rui Xia et al.   PLANT CELL

The Arabidopsis miR396 mediates pathogen-associated molecular pattern-triggered immune responses against fungal pathogens

(2017) Mauricio Soto-Suárez et al.   Scientific Reports

Identification, Characterization, and Functional Validation of Drought-responsive MicroRNAs in Subtropical Maize Inbreds

(2017) Jayaraman Aravind et al.   Frontiers in Plant Science

MicroRNA and Transcription Factor: Key Players in Plant Regulatory Network

(2017) Abdul F. A. Samad et al.   Frontiers in Plant Science

MicroRNA-like RNAs in plant pathogenic fungus Fusarium oxysporum f. sp. niveum are involved in toxin gene expression fine tuning

(2017) Xuefei Jiang et al.   3 Biotech

MicroRNA-like RNAs in plant pathogenic fungus Fusarium oxysporum f. sp. niveum are involved in toxin gene expression fine tuning

(2017) Xuefei Jiang et al.   3 Biotech

Dynamic changes of small RNAs in rice spikelet development reveal specialized reproductive phasiRNA pathways

(2016) Qili Fei et al.   JOURNAL OF EXPERIMENTAL BOTANY

Biogenesis of diverse plant phasiRNAs involves an miRNA-trigger and Dicer-processing

(2016) Reina Komiya   JOURNAL OF PLANT RESEARCH

Small RNAs Add Zing to the Zig-Zag-Zig Model of Plant Defenses

(2016) Qili Fei et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Uncovering leaf rust responsive miRNAs in wheat (Triticum aestivum L.) using high-throughput sequencing and prediction of their targets through degradome analysis

(2016) Dhananjay Kumar et al.   PLANTA

PMS1T, producing phased small-interfering RNAs, regulates photoperiod-sensitive male sterility in rice

(2016) Yourong Fan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Allelic barley MLA immune receptors recognize sequence-unrelated avirulence effectors of the powdery mildew pathogen

(2016) Xunli Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small RNAs regulate plant responses to filamentous pathogens

(2016) Tung Kuan et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

MicroRNAs in Rice Innate Immunity

(2016) Patricia Baldrich et al.   Rice

An LRR/Malectin Receptor-Like Kinase Mediates Resistance to Non-adapted and Adapted Powdery Mildew Fungi in Barley and Wheat

(2016) Jeyaraman Rajaraman 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

A dynamic evolutionary and functional landscape of plant phased small interfering RNAs

(2015) Yi Zheng et al.   BMC BIOLOGY

Evolution of the EKA family of powdery mildew avirulence-effector genes from the ORF 1 of a LINE retrotransposon

(2015) Joelle Amselem et al.   BMC GENOMICS

The role of plant small RNAs in NB-LRR regulation

(2015) June Hyun Park et al.   Briefings in Functional Genomics

MicroRNAs in Control of Plant Development

(2015) Chao Li et al.   JOURNAL OF CELLULAR PHYSIOLOGY

Secondary siRNAs fromMedicago NB-LRRsmodulated via miRNA-target interactions and their abundances

(2015) Qili Fei et al.   PLANT JOURNAL

Identification of eight effector candidate genes involved in early aggressiveness of the barley powdery mildew fungus

(2015) G. B. Aguilar et al.   PLANT PATHOLOGY

Constitutive Expression of RiceMicroRNA528Alters Plant Development and Enhances Tolerance to Salinity Stress and Nitrogen Starvation in Creeping Bentgrass

(2015) Shuangrong Yuan et al.   PLANT PHYSIOLOGY

The Barley Powdery Mildew Candidate Secreted Effector Protein CSEP0105 Inhibits the Chaperone Activity of a Small Heat Shock Protein

(2015) Ali Abdurehim Ahmed et al.   PLANT PHYSIOLOGY

Spatiotemporally dynamic, cell-type–dependent premeiotic and meiotic phasiRNAs in maize anthers

(2015) Jixian Zhai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The miRNA Interactome in Metabolic Homeostasis

(2015) Sean M. Hartig et al.   TRENDS IN ENDOCRINOLOGY AND METABOLISM

Battles and hijacks: noncoding transcription in plants

(2015) Federico Ariel et al.   TRENDS IN PLANT SCIENCE

Maize miRNA and target regulation in response to hormone depletion and light exposure during somatic embryogenesis

(2015) Elva C. Chávez-Hernández et al.   Frontiers in Plant Science

Biogenesis of trans-acting siRNAs, endogenous secondary siRNAs in plants

(2015) Manabu Yoshikawa   GENES & GENETIC SYSTEMS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

In silico analysis of the core signaling proteome from the barley powdery mildew pathogen (Blumeria graminis f.sp. hordei)

(2014) Stefan Kusch et al.   BMC GENOMICS

Identification and Analysis of Powdery Mildew-Responsive miRNAs in Wheat

(2014) Fangli Wu et al.   JOURNAL OF PHYTOPATHOLOGY

Growth–Defense Tradeoffs in Plants: A Balancing Act to Optimize Fitness

(2014) Bethany Huot et al.   Molecular Plant

sPARTA: a parallelized pipeline for integrated analysis of plant miRNA and cleaved mRNA data sets, including new miRNA target-identification software

(2014) Atul Kakrana et al.   NUCLEIC ACIDS RESEARCH

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

An Atlas of Soybean Small RNAs Identifies Phased siRNAs from Hundreds of Coding Genes

(2014) Siwaret Arikit et al.   PLANT CELL

Genome-Wide Discovery and Analysis of Phased Small Interfering RNAs in Chinese Sacred Lotus

(2014) Yun Zheng et al.   PLoS One

Plant pattern-recognition receptors

(2014) Cyril Zipfel   TRENDS IN IMMUNOLOGY

The miR9863 Family Regulates Distinct Mla Alleles in Barley to Attenuate NLR Receptor-Triggered Disease Resistance and Cell-Death Signaling

(2014) Jie Liu et al.   PLoS Genetics

Construction of small RNA-mediated gene regulatory networks in the roots of rice (Oryza sativa)

(2013) Xiaoxia Ma et al.   BMC GENOMICS

Over-expression of microRNA171 affects phase transitions and floral meristem determinancy in barley

(2013) Julien Curaba et al.   BMC PLANT BIOLOGY

Biogenesis and function of rice small RNAs from non-coding RNA precursors

(2013) Siwaret Arikit et al.   CURRENT OPINION IN PLANT BIOLOGY

Rapid construction of parallel analysis of RNA end (PARE) libraries for Illumina sequencing

(2013) Jixian Zhai et al.   METHODS

Roles of Plant Hormones and Their Interplay in Rice Immunity

(2013) Dong-Lei Yang et al.   Molecular Plant

The target gene of tae-miR164, a novel NAC transcription factor from the NAM subfamily, negatively regulates resistance of wheat to stripe rust

(2013) Hao Feng et al.   MOLECULAR PLANT PATHOLOGY

Host-Induced Gene Silencing in Barley Powdery Mildew Reveals a Class of Ribonuclease-Like Effectors

(2013) Clara Pliego et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Mla-andRom1-mediated control of microRNA398 and chloroplast copper/zinc superoxide dismutase regulates cell death in response to the barley powdery mildew fungus

(2013) Weihui Xu et al.   NEW PHYTOLOGIST

Identification of a novel microRNA (miRNA) from rice that targets an alternatively spliced transcript of theNramp6(Natural resistance-associated macrophage protein 6) gene involved in pathogen resistance

(2013) Sonia Campo et al.   NEW PHYTOLOGIST

Phased, Secondary, Small Interfering RNAs in Posttranscriptional Regulatory Networks

(2013) Q. Fei et al.   PLANT CELL

MicroRNA mediated regulation of metal toxicity in plants: present status and future perspectives

(2013) O. P. Gupta et al.   PLANT MOLECULAR BIOLOGY

ShortStack: Comprehensive annotation and quantification of small RNA genes

(2013) M. J. Axtell   RNA

Identification of Wheat Gene Sr35 That Confers Resistance to Ug99 Stem Rust Race Group

(2013) C. Saintenac et al.   SCIENCE

Transgenerational gene silencing causes gain of virulence in a plant pathogen

(2013) Dinah Qutob et al.   Nature Communications

Disease resistance or growth: the role of plant hormones in balancing immune responses and fitness costs

(2013) Nicolas Denancé et al.   Frontiers in Plant Science

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Structure and evolution of barley powdery mildew effector candidates

(2012) Carsten Pedersen et al.   BMC GENOMICS

Molecular Identification and Analysis of Arsenite Stress-Responsive miRNAs in Rice

(2012) Qingpo Liu et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Interaction of barley powdery mildew effector candidate CSEP0055 with the defence protein PR17c

(2012) Wen-Jing Zhang et al.   MOLECULAR PLANT PATHOLOGY

Molecular Crosstalk Between PAMP-Triggered Immunity and Photosynthesis

(2012) Vera Göhre et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Barley ROP Binding Kinase1 Is Involved in Microtubule Organization and in Basal Penetration Resistance to the Barley Powdery Mildew Fungus

(2012) C. Huesmann et al.   PLANT PHYSIOLOGY

Involvement of microRNA-Mediated Gene Expression Regulation in the Pathological Development of Stem Canker Disease in Populus trichocarpa

(2012) Jia-Ping Zhao et al.   PLoS One

microRNAs Associated with Drought Response in the Bioenergy Crop Sugarcane (Saccharum spp.)

(2012) Thaís Helena Ferreira et al.   PLoS One

Evidence for Small RNAs Homologous to Effector-Encoding Genes and Transposable Elements in the Oomycete Phytophthora infestans

(2012) Ramesh R. Vetukuri et al.   PLoS One

Functions of microRNAs in plant stress responses

(2012) Ramanjulu Sunkar et al.   TRENDS IN PLANT SCIENCE

Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants

(2011) Basel Khraiwesh et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

miRDeep-P: a computational tool for analyzing the microRNA transcriptome in plants

(2011) Xiaozeng Yang et al.   BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Identification of novel soybean microRNAs involved in abiotic and biotic stresses

(2011) Franceli R Kulcheski et al.   BMC GENOMICS

Microarray profiling reveals microRNAs involving soybean resistance to Phytophthora sojae

(2011) Na Guo et al.   GENOME

Regulation of basal resistance by a powdery mildew-induced cysteine-rich receptor-like protein kinase in barley

(2011) CBGOWDA RAYAPURAM et al.   MOLECULAR PLANT PATHOLOGY

Quantitative and Temporal Definition of theMlaTranscriptional Regulon During Barley–Powdery Mildew Interactions

(2011) Matthew J. Moscou et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

MiR398 and plant stress responses

(2011) Cheng Zhu et al.   PHYSIOLOGIA PLANTARUM

MicroRNA networks and developmental plasticity in plants

(2011) Ignacio Rubio-Somoza et al.   TRENDS IN PLANT SCIENCE

Identification and expression analysis of microRNAs and targets in the biofuel crop sugarcane

(2010) Almir S Zanca et al.   BMC PLANT BIOLOGY

Diverse set of microRNAs are responsive to powdery mildew infection and heat stress in wheat (Triticum aestivum L.)

(2010) Mingming Xin et al.   BMC PLANT BIOLOGY

miR396-targeted AtGRF transcription factors are required for coordination of cell division and differentiation during leaf development in Arabidopsis

(2010) Li Wang et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

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

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

Identification and analysis of seven H2O2-responsive miRNAs and 32 new miRNAs in the seedlings of rice (Oryza sativa L. ssp. indica)

(2010) Tian Li et al.   NUCLEIC ACIDS RESEARCH

Biotic stress globally downregulates photosynthesis genes

(2010) DAMLA D. BILGIN et al.   PLANT CELL AND ENVIRONMENT

Identification of MicroRNAs Involved in Pathogen-Associated Molecular Pattern-Triggered Plant Innate Immunity

(2010) Y. Li et al.   PLANT PHYSIOLOGY

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

(2010) P. D. Spanu et al.   SCIENCE

miR156-Regulated SPL Transcription Factors Define an Endogenous Flowering Pathway in Arabidopsis thaliana

(2009) Jia-Wei Wang et al.   CELL

Clusters and superclusters of phased small RNAs in the developing inflorescence of rice

(2009) C. Johnson et al.   GENOME RESEARCH

Distinct extremely abundant siRNAs associated with cosuppression in petunia

(2009) E. De Paoli et al.   RNA

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets

(2008) C. Addo-Quaye et al.   BIOINFORMATICS

Systematic functional analysis of calcium-signalling proteins in the genome of the rice-blast fungus,Magnaporthe oryzae, using a high-throughput RNA-silencing system

(2008) Quoc Bao Nguyen et al.   MOLECULAR MICROBIOLOGY

Global identification of microRNA–target RNA pairs by parallel analysis of RNA ends

(2008) Marcelo A German et al.   NATURE BIOTECHNOLOGY

Blufensin1 Negatively Impacts Basal Defense in Response to Barley Powdery Mildew

(2008) Y. Meng et al.   PLANT PHYSIOLOGY

Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs)

(2008) C. Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA