Dicer-like proteins influence Arabidopsis root microbiota independent of RNA-directed DNA methylation

A predatory myxobacterium controls cucumber Fusarium wilt by regulating the soil microbial community

(2020) Xianfeng Ye et al.   Microbiome

Critical function of DNA methyltransferase 1 in tomato development and regulation of the DNA methylome and transcriptome

(2019) Yu Yang et al.   Journal of Integrative Plant Biology

PRX9 and PRX40 are extensin peroxidases essential for maintaining tapetum and microspore cell wall integrity during Arabidopsis anther development

(2019) Joseph R Jacobowitz et al.   PLANT CELL

Alanine dehydrogenase and its applications – A review

(2019) Ushmaben Chandrakantbhai Dave et al.   CRITICAL REVIEWS IN BIOTECHNOLOGY

Plant intraspecific variation modulates nutrient cycling through its below ground rhizospheric microbiome

(2019) Leticia Pérez‐Izquierdo et al.   JOURNAL OF ECOLOGY

Plant-derived coumarins shape the composition of an Arabidopsis synthetic root microbiome

(2019) Mathias J. E. E. E. Voges et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Small RNAs – Big Players in Plant-Microbe Interactions

(2019) Chien-Yu Huang et al.   Cell Host & Microbe

Plant-Microbe Interactions Facing Environmental Challenge

(2019) Yu Ti Cheng et al.   Cell Host & Microbe

Roles of Plant-Derived Secondary Metabolites during Interactions with Pathogenic and Beneficial Microbes under Conditions of Environmental Stress

(2019) Kei Hiruma   Microorganisms

Rhizobacterium‐derived diacetyl modulates plant immunity in a phosphate‐dependent manner

(2019) Rafael JL Morcillo et al.   EMBO JOURNAL

Molecular networks in plant-pathogen holobiont

(2018) Tatsuya Nobori et al.   FEBS LETTERS

Cell wall extensins in root–microbe interactions and root secretions

(2018) Romain Castilleux et al.   JOURNAL OF EXPERIMENTAL BOTANY

Dynamics and function of DNA methylation in plants

(2018) Huiming Zhang et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Plant cell wall-mediated immunity: cell wall changes trigger disease resistance responses

(2018) Laura Bacete et al.   PLANT JOURNAL

MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health

(2018) Ioannis A. Stringlis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Large-scale replicated field study of maize rhizosphere identifies heritable microbes

(2018) William A. Walters et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The plant cell wall integrity maintenance and immune signaling systems cooperate to control stress responses inArabidopsis thaliana

(2018) Timo Engelsdorf et al.   Science Signaling

Feed Your Friends: Do Plant Exudates Shape the Root Microbiome?

(2018) Joelle Sasse et al.   TRENDS IN PLANT SCIENCE

The plant cell wall integrity maintenance and immune signaling systems cooperate to control stress responses inArabidopsis thaliana

(2018) Timo Engelsdorf et al.   Science Signaling

Structure and Reaction Mechanism of the LigJ Hydratase: An Enzyme Critical for the Bacterial Degradation of Lignin in the Protocatechuate 4,5-Cleavage Pathway

(2018) Tessily N. Hogancamp et al.   BIOCHEMISTRY

Microbial Interkingdom Interactions in Roots Promote Arabidopsis Survival

(2018) Paloma Durán et al.   CELL

Rhizosphere microbiome structure alters to enable wilt resistance in tomato

(2018) Min-Jung Kwak et al.   NATURE BIOTECHNOLOGY

Drought and host selection influence bacterial community dynamics in the grass root microbiome

(2017) Dan Naylor et al.   ISME Journal

The siRNA suppressor RTL1 is redox-regulated through glutathionylation of a conserved cysteine in the double-stranded-RNA-binding domain

(2017) Cyril Charbonnel et al.   NUCLEIC ACIDS RESEARCH

Small molecules below-ground: the role of specialized metabolites in the rhizosphere

(2017) Hassan Massalha et al.   PLANT JOURNAL

New discoveries generate new questions about RNA-directed DNA methylation in Arabidopsis

(2017) Huiming Zhang et al.   National Science Review

A Dicer-Independent Route for Biogenesis of siRNAs that Direct DNA Methylation in Arabidopsis

(2016) Ruiqiang Ye et al.   MOLECULAR CELL

Double-stranded RNAs induce a pattern-triggered immune signaling pathway in plants

(2016) Annette Niehl et al.   NEW PHYTOLOGIST

The role of DNA (de)methylation in immune responsiveness of Arabidopsis

(2016) Ana López Sánchez et al.   PLANT JOURNAL

The Soil-Borne Supremacy

(2016) Corné M.J. Pieterse et al.   TRENDS IN PLANT SCIENCE

Metabolomics in the Rhizosphere: Tapping into Belowground Chemical Communication

(2016) Nicole M. van Dam et al.   TRENDS IN PLANT SCIENCE

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

(2016) Wei Shen et al.   PLoS One

Roots Shaping Their Microbiome: Global Hotspots for Microbial Activity

(2015) Barbara Reinhold-Hurek et al.   Annual Review of Phytopathology

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

(2015) Dinghua Li et al.   BIOINFORMATICS

A One Precursor One siRNA Model for Pol IV-Dependent siRNA Biogenesis

(2015) Jixian Zhai et al.   CELL

Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley

(2015) Davide Bulgarelli et al.   Cell Host & Microbe

Dicer-independent RNA-directed DNA methylation in Arabidopsis

(2015) Dong-Lei Yang et al.   CELL RESEARCH

Iron-Dependent Callose Deposition Adjusts Root Meristem Maintenance to Phosphate Availability

(2015) Jens Müller et al.   DEVELOPMENTAL CELL

Non-targeted profiling of semi-polar metabolites in Arabidopsis root exudates uncovers a role for coumarin secretion and lignification during the local response to phosphate limitation

(2015) Jörg Ziegler et al.   JOURNAL OF EXPERIMENTAL BOTANY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Salicylic acid modulates colonization of the root microbiome by specific bacterial taxa

(2015) S. L. Lebeis et al.   SCIENCE

What lies beneath: belowground defense strategies in plants

(2015) Barbara De Coninck et al.   TRENDS IN PLANT SCIENCE

Comparative metabolomic analysis highlights the involvement of sugars and glycerol in melatonin-mediated innate immunity against bacterial pathogen in Arabidopsis

(2015) Yongqiang Qian et al.   Scientific Reports

Identification of Pol IV and RDR2-dependent precursors of 24 nt siRNAs guiding de novo DNA methylation in Arabidopsis

(2015) Todd Blevins et al.   eLife

Associations with rhizosphere bacteria can confer an adaptive advantage to plants

(2015) Cara H. Haney et al.   Nature Plants

The Diversity, Biogenesis, and Activities of Endogenous Silencing Small RNAs inArabidopsis

(2014) Nicolas G. Bologna et al.   Annual Review of Plant Biology

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Detection of Pol IV/RDR2-dependent transcripts at the genomic scale inArabidopsisreveals features and regulation of siRNA biogenesis

(2014) Shaofang Li et al.   GENOME RESEARCH

An Rrp6-like Protein Positively Regulates Noncoding RNA Levels and DNA Methylation in Arabidopsis

(2014) Huiming Zhang et al.   MOLECULAR CELL

Bacterial Communities Associated with the Leaves and the Roots of Arabidopsis thaliana

(2013) Natacha Bodenhausen et al.   PLoS One

Dynamics and biological relevance of DNA demethylation in Arabidopsis antibacterial defense

(2013) A. Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Quantitative divergence of the bacterial root microbiota in Arabidopsis thaliana relatives

(2013) K. Schlaeppi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Plant growth in Arabidopsis is assisted by compost soil-derived microbial communities

(2013) Lilia C. Carvalhais et al.   Frontiers in Plant Science

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(2012) Alexander Dobin et al.   BIOINFORMATICS

RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats

(2012) Tzuu-fen Lee et al.   Epigenetics

Metabolite fingerprinting of barley whole seeds, endosperms, and embryos during industrial malting

(2012) K. Gorzolka et al.   JOURNAL OF BIOTECHNOLOGY

Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota

(2012) Davide Bulgarelli et al.   NATURE

Sulfamethazine Suppresses Epigenetic Silencing in Arabidopsis by Impairing Folate Synthesis

(2012) H. Zhang et al.   PLANT CELL

Oleic Acid–Dependent Modulation of NITRIC OXIDE ASSOCIATED1 Protein Levels Regulates Nitric Oxide–Mediated Defense Signaling inArabidopsis

(2012) Mihir Kumar Mandal et al.   PLANT CELL

Widespread dynamic DNA methylation in response to biotic stress

(2012) R. H. Dowen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Modularity of methylotrophy, revisited

(2011) Ludmila Chistoserdova   ENVIRONMENTAL MICROBIOLOGY

The RNA Silencing Enzyme RNA Polymerase V Is Required for Plant Immunity

(2011) Ana López et al.   PLoS Genetics

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

miRBase: integrating microRNA annotation and deep-sequencing data

(2010) A. Kozomara et al.   NUCLEIC ACIDS RESEARCH

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

(2010) Y. Li et al.   PLANT PHYSIOLOGY

Plant-Growth-Promoting Rhizobacteria

(2009) Ben Lugtenberg et al.   Annual Review of Microbiology

ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes

(2009) Erik Kristiansson et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

PMRD: plant microRNA database

(2009) Zhenhai Zhang et al.   NUCLEIC ACIDS RESEARCH

Pectin, a versatile polysaccharide present in plant cell walls

(2009) Alphons G. J. Voragen et al.   STRUCTURAL CHEMISTRY

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Reduced V-ATPase Activity in the trans-Golgi Network Causes Oxylipin-Dependent Hypocotyl Growth Inhibition in Arabidopsis

(2008) A. Brux et al.   PLANT CELL

BAH1/NLA, a RING-Type Ubiquitin E3 Ligase, Regulates the Accumulation of Salicylic Acid and Immune Responses to Pseudomonas syringae DC3000

(2008) T. Yaeno et al.   PLANT PHYSIOLOGY

A Glucosinolate Metabolism Pathway in Living Plant Cells Mediates Broad-Spectrum Antifungal Defense

(2008) P. Bednarek et al.   SCIENCE