RNA-seq Transcriptional Profiling of an Arbuscular Mycorrhiza Provides Insights into Regulated and Coordinated Gene Expression inLotus japonicusandRhizophagus irregularis

Network of GRAS Transcription Factors Involved in the Control of Arbuscule Development inLotus japonicus

(2015) Li Xue et al.   PLANT PHYSIOLOGY

The concordance between RNA-seq and microarray data depends on chemical treatment and transcript abundance

(2014) Charles Wang et al.   NATURE BIOTECHNOLOGY

The Bifunctional Plant Receptor, OsCERK1, Regulates Both Chitin-Triggered Immunity and Arbuscular Mycorrhizal Symbiosis in Rice

(2014) Kana Miyata et al.   PLANT AND CELL PHYSIOLOGY

OPT3 Is a Phloem-Specific Iron Transporter That Is Essential for Systemic Iron Signaling and Redistribution of Iron and Cadmium in Arabidopsis

(2014) Z. Zhai et al.   PLANT CELL

The H+-ATPase HA1 of Medicago truncatula Is Essential for Phosphate Transport and Plant Growth during Arbuscular Mycorrhizal Symbiosis

(2014) F. Krajinski et al.   PLANT CELL

A H+-ATPase That Energizes Nutrient Uptake during Mycorrhizal Symbioses in Rice and Medicago truncatula

(2014) E. Wang et al.   PLANT CELL

The receptor kinaseCERK1has dual functions in symbiosis and immunity signalling

(2014) Xiaowei Zhang et al.   PLANT JOURNAL

Fatty acid synthesis and lipid metabolism in the obligate biotrophic fungusRhizophagus irregularisduring mycorrhization ofLotus japonicus

(2014) Vera Wewer et al.   PLANT JOURNAL

Gibberellins Interfere with Symbiosis Signaling and Gene Expression and Alter Colonization by Arbuscular Mycorrhizal Fungi inLotus japonicus

(2014) Naoya Takeda et al.   PLANT PHYSIOLOGY

Systematic Identification and Evolutionary Analysis of Catalytically Versatile Cytochrome P450 Monooxygenase Families Enriched in Model Basidiomycete Fungi

(2014) Khajamohiddin Syed et al.   PLoS One

Single Nucleus Genome Sequencing Reveals High Similarity among Nuclei of an Endomycorrhizal Fungus

(2014) Kui Lin et al.   PLoS Genetics

Cell and Developmental Biology of Arbuscular Mycorrhiza Symbiosis

(2013) Caroline Gutjahr et al.   Annual Review of Cell and Developmental Biology

Detecting small plant peptides using SPADA (Small Peptide Alignment Discovery Application)

(2013) Peng Zhou et al.   BMC BIOINFORMATICS

TCC: an R package for comparing tag count data with robust normalization strategies

(2013) Jianqiang Sun et al.   BMC BIOINFORMATICS

Expression changes of ribosomal proteins in phosphate- and iron-deficient Arabidopsis roots predict stress-specific alterations in ribosome composition

(2013) Jinyan Wang et al.   BMC GENOMICS

A roadmap of cell-type specific gene expression during sequential stages of the arbuscular mycorrhiza symbiosis

(2013) Claudia Hogekamp et al.   BMC GENOMICS

An endogenous artificial microRNA system for unraveling the function of root endosymbioses related genes in Medicago truncatula

(2013) Emanuel A Devers et al.   BMC PLANT BIOLOGY

A DELLA protein complex controls the arbuscular mycorrhizal symbiosis in plants

(2013) Nan Yu et al.   CELL RESEARCH

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

NSP1 is a component of the Myc signaling pathway

(2013) Pierre-Marc Delaux et al.   NEW PHYTOLOGIST

Short-chain chitin oligomers from arbuscular mycorrhizal fungi trigger nuclear Ca2+spiking inMedicago truncatularoots and their production is enhanced by strigolactone

(2013) Andrea Genre et al.   NEW PHYTOLOGIST

Combined phosphate and nitrogen limitation generates a nutrient stress transcriptome favorable for arbuscular mycorrhizal symbiosis inMedicago truncatula

(2013) Laurent Bonneau et al.   NEW PHYTOLOGIST

PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors

(2013) Jinpu Jin et al.   NUCLEIC ACIDS RESEARCH

CERBERUS and NSP1 of Lotus japonicus are Common Symbiosis Genes that Modulate Arbuscular Mycorrhiza Development

(2013) Naoya Takeda et al.   PLANT AND CELL PHYSIOLOGY

LjMATE1: A Citrate Transporter Responsible for Iron Supply to the Nodule Infection Zone of Lotus japonicus

(2013) Kojiro Takanashi et al.   PLANT AND CELL PHYSIOLOGY

The C2H2 Transcription Factor REGULATOR OF SYMBIOSOME DIFFERENTIATION Represses Transcription of the Secretory Pathway Gene VAMP721a and Promotes Symbiosome Development in Medicago truncatula

(2013) S. Sinharoy et al.   PLANT CELL

A tandem Kunitz protease inhibitor (KPI106)-serine carboxypeptidase (SCP1) controls mycorrhiza establishment and arbuscule development inMedicago truncatula

(2013) Stefanie S. Rech et al.   PLANT JOURNAL

Thecis-acting CTTC-P1BS module is indicative for gene function ofLjVTI12, a Qb-SNARE protein gene that is required for arbuscule formation inLotus japonicus

(2013) Frédéric Lota et al.   PLANT JOURNAL

A Nodule-Specific Lipid Transfer Protein AsE246 Participates in Transport of Plant-Synthesized Lipids to Symbiosome Membrane and Is Essential for Nodule Organogenesis in Chinese Milk Vetch

(2013) L. Lei et al.   PLANT PHYSIOLOGY

Spatio-Temporal Expression Patterns of Arabidopsis thaliana and Medicago truncatula Defensin-Like Genes

(2013) Mesfin Tesfaye et al.   PLoS One

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

DELLA proteins regulate arbuscule formation in arbuscular mycorrhizal symbiosis

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

Root-derived CLE glycopeptides control nodulation by direct binding to HAR1 receptor kinase

(2013) Satoru Okamoto et al.   Nature Communications

Iron: an essential micronutrient for the legume-rhizobium symbiosis

(2013) Ella M. Brear et al.   Frontiers in Plant Science

Strategies for transcriptome analysis in nonmodel plants

(2012) Judson A. Ward et al.   AMERICAN JOURNAL OF BOTANY

Optimizing illumina next-generation sequencing library preparation for extremely at-biased genomes

(2012) Samuel O Oyola et al.   BMC GENOMICS

The non-specific lipid transfer protein N5 of Medicago truncatula is implicated in epidermal stages of rhizobium-host interaction

(2012) Youry Pii et al.   BMC PLANT BIOLOGY

Two putative-aquaporin genes are differentially expressed during arbuscular mycorrhizal symbiosis in Lotus japonicus

(2012) Marco Giovannetti et al.   BMC PLANT BIOLOGY

A GRAS-Type Transcription Factor with a Specific Function in Mycorrhizal Signaling

(2012) Enrico Gobbato et al.   CURRENT BIOLOGY

A Common Signaling Process that Promotes Mycorrhizal and Oomycete Colonization of Plants

(2012) Ertao Wang et al.   CURRENT BIOLOGY

Inhibition of Glutamine Synthetase by Phosphinothricin Leads to Transcriptome Reprograming in Root Nodules ofMedicago truncatula

(2012) Ana R. Seabra et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Specialized ribosomes: a new frontier in gene regulation and organismal biology

(2012) Shifeng Xue et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Nonredundant Regulation of Rice Arbuscular Mycorrhizal Symbiosis by Two Members of thePHOSPHATE TRANSPORTER1Gene Family

(2012) Shu-Yi Yang et al.   PLANT CELL

The microRNA miR171h modulates arbuscular mycorrhizal colonization ofMedicago truncatulaby targetingNSP2

(2012) Dominique Lauressergues et al.   PLANT JOURNAL

An AM-induced,MYB-family gene ofLotus japonicus(LjMAMI) affects root growth in an AM-independent manner

(2012) Veronica Volpe et al.   PLANT JOURNAL

Medicago truncatula ERN Transcription Factors: Regulatory Interplay with NSP1/NSP2 GRAS Factors and Expression Dynamics throughout Rhizobial Infection

(2012) M. R. Cerri et al.   PLANT PHYSIOLOGY

Transcriptional Responses toward Diffusible Signals from Symbiotic Microbes Reveal MtNFP- and MtDMI3-Dependent Reprogramming of Host Gene Expression by Arbuscular Mycorrhizal Fungal Lipochitooligosaccharides

(2012) L. F. Czaja et al.   PLANT PHYSIOLOGY

Heart of Endosymbioses: Transcriptomics Reveals a Conserved Genetic Program among Arbuscular Mycorrhizal, Actinorhizal and Legume-Rhizobial Symbioses

(2012) Alexandre Tromas et al.   PLoS One

Rhizobium-legume symbiosis shares an exocytotic pathway required for arbuscule formation

(2012) S. Ivanov et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolution of the Land Plant Exocyst Complexes

(2012) Fatima Cvrčková et al.   Frontiers in Plant Science

Transcriptional regulation of defence genes and involvement of the WRKY transcription factor in arbuscular mycorrhizal potato root colonization

(2011) Adrien Gallou et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Search for nodulation-related CLE genes in the genome of Glycine max

(2011) Virginie Mortier et al.   JOURNAL OF EXPERIMENTAL BOTANY

Inoculation- and Nitrate-Induced CLE Peptides of Soybean Control NARK-Dependent Nodule Formation

(2011) Dugald E. Reid et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

The transcriptome of the arbuscular mycorrhizal fungus Glomus intraradices (DAOM 197198) reveals functional tradeoffs in an obligate symbiont

(2011) E. Tisserant et al.   NEW PHYTOLOGIST

Soybean Nodule-Enhanced CLE Peptides in Roots Act as Signals in GmNARK-Mediated Nodulation Suppression

(2011) Chae Woo Lim et al.   PLANT AND CELL PHYSIOLOGY

The Integral Membrane Protein SEN1 is Required for Symbiotic Nitrogen Fixation in Lotus japonicus Nodules

(2011) Tsuneo Hakoyama et al.   PLANT AND CELL PHYSIOLOGY

Multiple Exocytotic Markers Accumulate at the Sites of Perifungal Membrane Biogenesis in Arbuscular Mycorrhizas

(2011) A. Genre et al.   PLANT AND CELL PHYSIOLOGY

Strigolactone Biosynthesis in Medicago truncatula and Rice Requires the Symbiotic GRAS-Type Transcription Factors NSP1 and NSP2

(2011) W. Liu et al.   PLANT CELL

Mycorrhizal symbiosis stimulates endoreduplication in angiosperms

(2011) L. D. BAINARD et al.   PLANT CELL AND ENVIRONMENT

Arbuscule-containing and non-colonized cortical cells of mycorrhizal roots undergo extensive and specific reprogramming during arbuscular mycorrhizal development

(2011) Nicole Gaude et al.   PLANT JOURNAL

The half-size ABC transporters STR1 and STR2 are indispensable for mycorrhizal arbuscule formation in rice

(2011) Caroline Gutjahr et al.   PLANT JOURNAL

Laser Microdissection Unravels Cell-Type-Specific Transcription in Arbuscular Mycorrhizal Roots, Including CAAT-Box Transcription Factor Gene Expression Correlating with Fungal Contact and Spread

(2011) C. Hogekamp et al.   PLANT PHYSIOLOGY

SCARECROW-LIKE 3 promotes gibberellin signaling by antagonizing master growth repressor DELLA in Arabidopsis

(2011) Zhong-Lin Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Trehalose-6-Phosphate: Connecting Plant Metabolism and Development

(2011) Jathish Ponnu et al.   Frontiers in Plant Science

Cytochrome P450 enzymes in the fungal kingdom

(2010) B. Črešnar et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Germin-like proteins (GLPs) in cereal genomes: gene clustering and dynamic roles in plant defence

(2010) James Breen et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Two CLE genes are induced by phosphate in roots of Lotus japonicus

(2010) Sachiko Funayama-Noguchi et al.   JOURNAL OF PLANT RESEARCH

Fungal lipochitooligosaccharide symbiotic signals in arbuscular mycorrhiza

(2010) Fabienne Maillet 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

Dynamics of Periarbuscular Membranes Visualized with a Fluorescent Phosphate Transporter in Arbuscular Mycorrhizal Roots of Rice

(2010) Yoshihiro Kobae et al.   PLANT AND CELL PHYSIOLOGY

NENA, a Lotus japonicus Homolog of Sec13, Is Required for Rhizodermal Infection by Arbuscular Mycorrhiza Fungi and Rhizobia but Dispensable for Cortical Endosymbiotic Development

(2010) M. Groth et al.   PLANT CELL

Two Medicago truncatula Half-ABC Transporters Are Essential for Arbuscule Development in Arbuscular Mycorrhizal Symbiosis

(2010) Q. Zhang et al.   PLANT CELL

Vapyrin, a gene essential for intracellular progression of arbuscular mycorrhizal symbiosis, is also essential for infection by rhizobia in the nodule symbiosis of Medicago truncatula

(2010) Jeremy D. Murray et al.   PLANT JOURNAL

The PAM1 gene of petunia, required for intracellular accommodation and morphogenesis of arbuscular mycorrhizal fungi, encodes a homologue of VAPYRIN

(2010) Nadja Feddermann et al.   PLANT JOURNAL

CLE Peptides Control Medicago truncatula Nodulation Locally and Systemically

(2010) V. Mortier et al.   PLANT PHYSIOLOGY

LysM-Type Mycorrhizal Receptor Recruited for Rhizobium Symbiosis in Nonlegume Parasponia

(2010) R. Op den Camp et al.   SCIENCE

Plant Peptides Govern Terminal Differentiation of Bacteria in Symbiosis

(2010) W. Van de Velde et al.   SCIENCE

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

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

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

Medicago truncatula and Glomus intraradices gene expression in cortical cells harboring arbuscules in the arbuscular mycorrhizal symbiosis

(2009) S Karen Gomez et al.   BMC PLANT BIOLOGY

The exocyst complex in polarized exocytosis

(2009) Bing He et al.   CURRENT OPINION IN CELL BIOLOGY

Plant lectins: the ties that bind in root symbiosis and plant defense

(2009) Peter L. De Hoff et al.   MOLECULAR GENETICS AND GENOMICS

Presymbiotic factors released by the arbuscular mycorrhizal fungusGigaspora margaritainduce starch accumulation inLotus japonicusroots

(2009) Caroline Gutjahr et al.   NEW PHYTOLOGIST

Genome-wide reprogramming of regulatory networks, transport, cell wall and membrane biogenesis during arbuscular mycorrhizal symbiosis in Lotus japonicus

(2009) Mike Guether et al.   NEW PHYTOLOGIST

Mycorrhizal associations and other means of nutrition of vascular plants: understanding the global diversity of host plants by resolving conflicting information and developing reliable means of diagnosis

(2009) Mark C. Brundrett   PLANT AND SOIL

Apoplastic plant subtilases support arbuscular mycorrhiza development inLotus japonicus

(2009) Naoya Takeda et al.   PLANT JOURNAL

Medicago truncatulaVapyrin is a novel protein required for arbuscular mycorrhizal symbiosis

(2009) Nathan Pumplin et al.   PLANT JOURNAL

A Mycorrhizal-Specific Ammonium Transporter from Lotus japonicus Acquires Nitrogen Released by Arbuscular Mycorrhizal Fungi

(2009) M. Guether et al.   PLANT PHYSIOLOGY

Genomic Inventory and Transcriptional Analysis of Medicago truncatula Transporters

(2009) V. A. Benedito et al.   PLANT PHYSIOLOGY

Dissection of Symbiosis and Organ Development by Integrated Transcriptome Analysis of Lotus japonicus Mutant and Wild-Type Plants

(2009) Niels Høgslund et al.   PLoS One

CLE peptide signaling during plant development

(2009) Guodong Wang et al.   PROTOPLASMA

A role for the ribosome in development

(2009) Mary E. Byrne   TRENDS IN PLANT SCIENCE

Fungal cytochrome P450 database

(2008) Jongsun Park et al.   BMC GENOMICS

Genome Structure of the Legume, Lotus japonicus

(2008) S. Sato et al.   DNA RESEARCH

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Arbuscular mycorrhiza: the mother of plant root endosymbioses

(2008) Martin Parniske   NATURE REVIEWS MICROBIOLOGY

Nod Factor/Nitrate-Induced CLE Genes that Drive HAR1-Mediated Systemic Regulation of Nodulation

(2008) Satoru Okamoto et al.   PLANT AND CELL PHYSIOLOGY

Prepenetration Apparatus Assembly Precedes and Predicts the Colonization Patterns of Arbuscular Mycorrhizal Fungi within the Root Cortex of Both Medicago truncatula and Daucus carota

(2008) A. Genre et al.   PLANT CELL

GR24, a Synthetic Analog of Strigolactones, Stimulates the Mitosis and Growth of the Arbuscular Mycorrhizal Fungus Gigaspora rosea by Boosting Its Energy Metabolism

(2008) A. Besserer et al.   PLANT PHYSIOLOGY

CYCLOPS, a mediator of symbiotic intracellular accommodation

(2008) K. Yano et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE