Microbial genome-enabled insights into plant–microorganism interactions

How Do Filamentous Pathogens Deliver Effector Proteins into Plant Cells?

(2014) Benjamin Petre et al.   PLOS BIOLOGY

A Synthetic Community Approach Reveals Plant Genotypes Affecting the Phyllosphere Microbiota

(2014) Natacha Bodenhausen et al.   PLoS Genetics

The genome sequence and effector complement of the flax rust pathogen Melampsora lini

(2014) Adnane Nemri et al.   Frontiers in Plant Science

Structure and Functions of the Bacterial Microbiota of Plants

(2013) Davide Bulgarelli et al.   Annual Review of Plant Biology

Extensive chromosomal reshuffling drives evolution of virulence in an asexual pathogen

(2013) R. de Jonge et al.   GENOME RESEARCH

Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants

(2013) Thomas R Turner et al.   ISME Journal

IDBA-MT: De Novo Assembler for Metatranscriptomic Data Generated from Next-Generation Sequencing Technology

(2013) Henry C.M. Leung et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Insights into the phylogeny and coding potential of microbial dark matter

(2013) Christian Rinke et al.   NATURE

The wheat powdery mildew genome shows the unique evolution of an obligate biotroph

(2013) Thomas Wicker et al.   NATURE GENETICS

Metagenomic species profiling using universal phylogenetic marker genes

(2013) Shinichi Sunagawa et al.   NATURE METHODS

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

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

Potential impact of soil microbiomes on the leaf metabolome and on herbivore feeding behavior

(2013) Dayakar V. Badri et al.   NEW PHYTOLOGIST

Host Genotype Shapes the Foliar Fungal Microbiome of Balsam Poplar (Populus balsamifera)

(2013) Miklós Bálint et al.   PLoS One

Receptor-like kinase SOBIR1/EVR interacts with receptor-like proteins in plant immunity against fungal infection

(2013) T. W. H. Liebrand et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Diversity and heritability of the maize rhizosphere microbiome under field conditions

(2013) J. A. Peiffer 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

Genome of an arbuscular mycorrhizal fungus provides insight into the oldest plant symbiosis

(2013) E. Tisserant et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mosaic genome structure of the barley powdery mildew pathogen and conservation of transcriptional programs in divergent hosts

(2013) S. Hacquard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hijacking of leguminous nodulation signaling by the rhizobial type III secretion system

(2013) S. Okazaki et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Unexpected Diversity during Community Succession in the Apple Flower Microbiome

(2013) A. Shade et al.   mBio

Two distinct secretion systems facilitate tissue invasion by the rice blast fungus Magnaporthe oryzae

(2013) Martha C. Giraldo et al.   Nature Communications

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2

(2012) Martin Wu et al.   BIOINFORMATICS

IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth

(2012) Y. Peng et al.   BIOINFORMATICS

Structure and evolution of barley powdery mildew effector candidates

(2012) Carsten Pedersen et al.   BMC GENOMICS

Extensive remodeling of the Pseudomonas syringae pv. avellanae type III secretome associated with two independent host shifts onto hazelnut

(2012) Heath E O’Brien et al.   BMC MICROBIOLOGY

Oomycetes, effectors, and all that jazz

(2012) Tolga O Bozkurt et al.   CURRENT OPINION IN PLANT BIOLOGY

Linking fungal communities in roots, rhizosphere, and soil to the health status ofPisum sativum

(2012) Lihui Xu et al.   FEMS MICROBIOLOGY ECOLOGY

Leaf microbiota in an agroecosystem: spatiotemporal variation in bacterial community composition on field-grown lettuce

(2012) Gurdeep Rastogi et al.   ISME Journal

Flagellin Perception Varies Quantitatively in Arabidopsis thaliana and Its Relatives

(2012) M. M. Vetter et al.   MOLECULAR BIOLOGY AND EVOLUTION

Defining the core Arabidopsis thaliana root microbiome

(2012) Derek S. Lundberg et al.   NATURE

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

(2012) Davide Bulgarelli et al.   NATURE

Who's who in the plant root microbiome?

(2012) Penny R Hirsch et al.   NATURE BIOTECHNOLOGY

Lifestyle transitions in plant pathogenic Colletotrichum fungi deciphered by genome and transcriptome analyses

(2012) Richard J O'Connell et al.   NATURE GENETICS

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Microbial life in the phyllosphere

(2012) Julia A. Vorholt   NATURE REVIEWS MICROBIOLOGY

Culturing a plant microbiome community at the cross-Rhodes

(2012) Sarah L. Lebeis et al.   NEW PHYTOLOGIST

MetaVelvet: an extension of Velvet assembler to de novo metagenome assembly from short sequence reads

(2012) Toshiaki Namiki et al.   NUCLEIC ACIDS RESEARCH

Fusion of two divergent fungal individuals led to the recent emergence of a unique widespread pathogen species

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

Identification of innate immunity elicitors using molecular signatures of natural selection

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

Tomato immune receptor Ve1 recognizes effector of multiple fungal pathogens uncovered by genome and RNA sequencing

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

High-throughput genomic sequencing of cassava bacterial blight strains identifies conserved effectors to target for durable resistance

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

The rhizosphere microbiome and plant health

(2012) Roeland L. Berendsen et al.   TRENDS IN PLANT SCIENCE

Comparative Genomics of Plant-Associated Pseudomonas spp.: Insights into Diversity and Inheritance of Traits Involved in Multitrophic Interactions

(2012) Joyce E. Loper et al.   PLoS Genetics

The Accessory Genome as a Cradle for Adaptive Evolution in Pathogens

(2012) Daniel Croll et al.   PLoS Pathogens

Ray Meta: scalable de novo metagenome assembly and profiling

(2012) Sébastien Boisvert et al.   GENOME BIOLOGY

Geographical Location Determines the Population Structure in Phyllosphere Microbial Communities of a Salt-Excreting Desert Tree

(2011) Omri M. Finkel et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Distinct Microbial Communities within the Endosphere and Rhizosphere of Populus deltoides Roots across Contrasting Soil Types

(2011) Neil R. Gottel et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

The Human Microbiome Project in 2011 and Beyond

(2011) Lita M. Proctor   Cell Host & Microbe

A Secreted Fungal Effector of Glomus intraradices Promotes Symbiotic Biotrophy

(2011) Silke Kloppholz et al.   CURRENT BIOLOGY

Pathogenomics of fungal plant parasites: what have we learnt about pathogenesis?

(2011) Sarah Maria Schmidt et al.   CURRENT OPINION IN PLANT BIOLOGY

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

The making of a new pathogen: Insights from comparative population genomics of the domesticated wheat pathogen Mycosphaerella graminicola and its wild sister species

(2011) E. H. Stukenbrock et al.   GENOME RESEARCH

Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice

(2011) Claudia Knief et al.   ISME Journal

Changes in spinach phylloepiphytic bacteria communities following minimal processing and refrigerated storage described using pyrosequencing of 16S rRNA amplicons

(2011) G. Lopez-Velasco et al.   JOURNAL OF APPLIED MICROBIOLOGY

The Microbial Phyllogeography of the Carnivorous Plant Sarracenia alata

(2011) Margaret M. Koopman et al.   MICROBIAL ECOLOGY

Distinctive Phyllosphere Bacterial Communities in Tropical Trees

(2011) Mincheol Kim et al.   MICROBIAL ECOLOGY

NLR functions in plant and animal immune systems: so far and yet so close

(2011) Takaki Maekawa et al.   NATURE IMMUNOLOGY

Taxonomic metagenome sequence assignment with structured output models

(2011) Kaustubh R Patil et al.   NATURE METHODS

BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing

(2011) Pavlo Lutsik et al.   NUCLEIC ACIDS RESEARCH

IMG/M: the integrated metagenome data management and comparative analysis system

(2011) V. M. Markowitz et al.   NUCLEIC ACIDS RESEARCH

Of PAMPs and Effectors: The Blurred PTI-ETI Dichotomy

(2011) Bart P.H.J. Thomma et al.   PLANT CELL

Comparative Metaproteomic Analysis on Consecutively Rehmannia glutinosa-Monocultured Rhizosphere Soil

(2011) Linkun Wu et al.   PLoS One

Dramatic Transcriptional Changes in an Intracellular Parasite Enable Host Switching between Plant and Insect

(2011) Kenro Oshima et al.   PLoS One

Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes

(2011) T. A. Richards et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phytoplasma protein effector SAP11 enhances insect vector reproduction by manipulating plant development and defense hormone biosynthesis

(2011) A. Sugio et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Obligate biotrophy features unraveled by the genomic analysis of rust fungi

(2011) S. Duplessis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial community assembly based on functional genes rather than species

(2011) C. Burke et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bacterial adaptation to life in association with plants - A proteomic perspective from culture to in situ conditions

(2011) Claudia Knief et al.   PROTEOMICS

Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria

(2011) R. Mendes et al.   SCIENCE

Effector diversification within compartments of the Leptosphaeria maculans genome affected by Repeat-Induced Point mutations

(2011) Thierry Rouxel et al.   Nature Communications

Gene Gain and Loss during Evolution of Obligate Parasitism in the White Rust Pathogen of Arabidopsis thaliana

(2011) Eric Kemen et al.   PLOS BIOLOGY

Dynamic Evolution of Pathogenicity Revealed by Sequencing and Comparative Genomics of 19 Pseudomonas syringae Isolates

(2011) David A. Baltrus et al.   PLoS Pathogens

Endophytic Life Strategies Decoded by Genome and Transcriptome Analyses of the Mutualistic Root Symbiont Piriformospora indica

(2011) Alga Zuccaro et al.   PLoS Pathogens

XanthomonasAvrBs3 Family-Type III Effectors: Discovery and Function

(2010) Jens Boch et al.   Annual Review of Phytopathology

The Carnivorous Pale Pitcher Plant Harbors Diverse, Distinct, and Time-Dependent Bacterial Communities

(2010) M. M. Koopman et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Computational prediction of type III secreted proteins from gram-negative bacteria

(2010) Yang Yang et al.   BMC BIOINFORMATICS

MLTreeMap - accurate Maximum Likelihood placement of environmental DNA sequences into taxonomic and functional reference phylogenies

(2010) Manuel Stark et al.   BMC GENOMICS

External Lipid PI3P Mediates Entry of Eukaryotic Pathogen Effectors into Plant and Animal Host Cells

(2010) Shiv D. Kale et al.   CELL

The ecology of the phyllosphere: geographic and phylogenetic variability in the distribution of bacteria on tree leaves

(2010) Amanda J. Redford et al.   ENVIRONMENTAL MICROBIOLOGY

Are root exudates more important than other sources of rhizodeposits in structuring rhizosphere bacterial communities?

(2010) Paul G. Dennis et al.   FEMS MICROBIOLOGY ECOLOGY

Site and plant species are important determinants of the Methylobacterium community composition in the plant phyllosphere

(2010) Claudia Knief et al.   ISME Journal

Characterization of Metaproteomics in Crop Rhizospheric Soil

(2010) Hai-Bin Wang et al.   JOURNAL OF PROTEOME RESEARCH

Identification and Functional Analysis of Type III Effector Proteins inMesorhizobium loti

(2010) Shin Okazaki et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Périgord black truffle genome uncovers evolutionary origins and mechanisms of symbiosis

(2010) Francis Martin et al.   NATURE

Comparative genomics reveals mobile pathogenicity chromosomes in Fusarium

(2010) Li-Jun Ma et al.   NATURE

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

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

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

What triggers grass endophytes to switch from mutualism to pathogenism?

(2010) Carla J. Eaton et al.   PLANT SCIENCE

Tomato Cf resistance proteins mediate recognition of cognate homologous effectors from fungi pathogenic on dicots and monocots

(2010) I. Stergiopoulos et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Signatures of Adaptation to Obligate Biotrophy in the Hyaloperonospora arabidopsidis Genome

(2010) L. Baxter et al.   SCIENCE

Pathogenicity Determinants in Smut Fungi Revealed by Genome Comparison

(2010) J. Schirawski et al.   SCIENCE

Genome Evolution Following Host Jumps in the Irish Potato Famine Pathogen Lineage

(2010) S. Raffaele et al.   SCIENCE

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

(2010) P. D. Spanu et al.   SCIENCE

Pyrosequencing reveals a contrasted bacterial diversity between oak rhizosphere and surrounding soil

(2010) Stéphane Uroz et al.   Environmental Microbiology Reports

Evolution of Linked Avirulence Effectors in Leptosphaeria maculans Is Affected by Genomic Environment and Exposure to Resistance Genes in Host Plants

(2010) Angela P. Van de Wouw et al.   PLoS Pathogens

A Renaissance of Elicitors: Perception of Microbe-Associated Molecular Patterns and Danger Signals by Pattern-Recognition Receptors

(2009) Thomas Boller et al.   Annual Review of Plant Biology

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Plant species and soil type cooperatively shape the structure and function of microbial communities in the rhizosphere

(2009) Gabriele Berg et al.   FEMS MICROBIOLOGY ECOLOGY

Bacterial Succession on the Leaf Surface: A Novel System for Studying Successional Dynamics

(2009) Amanda J. Redford et al.   MICROBIAL ECOLOGY

Phymm and PhymmBL: metagenomic phylogenetic classification with interpolated Markov models

(2009) Arthur Brady et al.   NATURE METHODS

Massively parallel 454 sequencing indicates hyperdiverse fungal communities in temperateQuercus macrocarpaphyllosphere

(2009) A. Jumpponen et al.   NEW PHYTOLOGIST

Association Genetics Reveals Three Novel Avirulence Genes from the Rice Blast Fungal Pathogen Magnaporthe oryzae

(2009) K. Yoshida et al.   PLANT CELL

An ABC Transporter Mutation Alters Root Exudation of Phytochemicals That Provoke an Overhaul of Natural Soil Microbiota

(2009) D. V. Badri et al.   PLANT PHYSIOLOGY

Prediction of Type III Secretion Signals in Genomes of Gram-Negative Bacteria

(2009) Martin Löwer et al.   PLoS One

Meiosis Drives Extraordinary Genome Plasticity in the Haploid Fungal Plant Pathogen Mycosphaerella graminicola

(2009) Alexander H. J. Wittenberg et al.   PLoS One

Community proteogenomics reveals insights into the physiology of phyllosphere bacteria

(2009) N. Delmotte et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Terrific Protein Traffic: The Mystery of Effector Protein Delivery by Filamentous Plant Pathogens

(2009) R. Panstruga et al.   SCIENCE

The targeting of plant cellular systems by injected type III effector proteins

(2009) Jennifer D. Lewis et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Establishing nitrogen-fixing symbiosis with legumes: how many rhizobium recipes?

(2009) Catherine Masson-Boivin et al.   TRENDS IN MICROBIOLOGY

The Genome of Nectria haematococca: Contribution of Supernumerary Chromosomes to Gene Expansion

(2009) Jeffrey J. Coleman et al.   PLoS Genetics

Sequence-Based Prediction of Type III Secreted Proteins

(2009) Roland Arnold et al.   PLoS Pathogens

Next-Generation DNA Sequencing Methods

(2008) Elaine R. Mardis   Annual Review of Genomics and Human Genetics

Rhizobial secreted proteins as determinants of host specificity in the rhizobium–legume symbiosis

(2008) Maarten Fauvart et al.   FEMS MICROBIOLOGY LETTERS

Genome sequence of the  -rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia

(2008) C. Amadou et al.   GENOME RESEARCH

Phyllosphere microbiology with special reference to diversity and plant genotype

(2008) J.M. Whipps et al.   JOURNAL OF APPLIED MICROBIOLOGY

Phytoplasmas: bacteria that manipulate plants and insects

(2008) SASKIA A. HOGENHOUT et al.   MOLECULAR PLANT PATHOLOGY

AY-WB Phytoplasma Secretes a Protein That Targets Plant Cell Nuclei

(2008) Xiaodong Bai et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

The genome of Laccaria bicolor provides insights into mycorrhizal symbiosis

(2008) F. Martin et al.   NATURE

Genetic Mapping in Human Disease

(2008) D. Altshuler et al.   SCIENCE

The Population Genetics of dN/dS

(2008) Sergey Kryazhimskiy et al.   PLoS Genetics

A simple, fast, and accurate method of phylogenomic inference

(2008) Martin Wu et al.   GENOME BIOLOGY