Comparative Transcriptomic Analysis of Two Actinorhizal Plants and the Legume Medicagotruncatula Supports the Homology of Root Nodule Symbioses and Is Congruent With a Two-Step Process of Evolution in the Nitrogen-Fixing Clade of Angiosperms

Comparative genomics of the nonlegumeParasponiareveals insights into evolution of nitrogen-fixing rhizobium symbioses

(2018) Robin van Velzen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis

(2018) Maximilian Griesmann et al.   SCIENCE

Determining the Site of Action of Strigolactones during Nodulation

(2017) Erin L. McAdam et al.   PLANT PHYSIOLOGY

A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny – The Legume Phylogeny Working Group (LPWG)

(2017) Nasim Azani et al.   TAXON

Cytokinins in Symbiotic Nodulation: When, Where, What For?

(2017) Pascal Gamas et al.   TRENDS IN PLANT SCIENCE

Comprehensive Analysis of DWARF14-LIKE2 (DLK2) Reveals Its Functional Divergence from Strigolactone-Related Paralogs

(2017) Attila Végh et al.   Frontiers in Plant Science

Chasing unicorns: Nodulation origins and the paradox of novelty

(2016) Jeff J. Doyle   AMERICAN JOURNAL OF BOTANY

An assemblage of Frankia Cluster II strains from California contains the canonical nod genes and also the sulfotransferase gene nodH

(2016) Thanh Van Nguyen et al.   BMC GENOMICS

Expansion of the Gene Ontology knowledgebase and resources

(2016)   NUCLEIC ACIDS RESEARCH

Strigolactone regulates shoot development through a core signalling pathway

(2016) Tom Bennett et al.   Biology Open

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

The strigolactone biosynthesis gene DWARF27 is co-opted in rhizobium symbiosis

(2015) Arjan van Zeijl et al.   BMC PLANT BIOLOGY

Rhizobium–legume symbiosis in the absence of Nod factors: two possible scenarios with or without the T3SS

(2015) Shin Okazaki et al.   ISME Journal

Hunting and hallucinogens: The use psychoactive and other plants to improve the hunting ability of dogs

(2015) Bradley C. Bennett et al.   JOURNAL OF ETHNOPHARMACOLOGY

KNOTTED1-LIKE HOMEOBOX 3: a new regulator of symbiotic nodule development

(2015) M. Azarakhsh et al.   JOURNAL OF EXPERIMENTAL BOTANY

Identification of Arabidopsis thaliana NRT1/PTR FAMILY (NPF) proteins capable of transporting plant hormones

(2015) Yasutaka Chiba et al.   JOURNAL OF PLANT RESEARCH

Rhizobium Lipo-chitooligosaccharide Signaling Triggers Accumulation of Cytokinins in Medicago truncatula Roots

(2015) Arjan van Zeijl et al.   Molecular Plant

Bacterial-induced calcium oscillations are common to nitrogen-fixing associations of nodulating legumes and non-legumes

(2015) Emma Granqvist et al.   NEW PHYTOLOGIST

TheCasuarina NINgene is transcriptionally activated throughoutFrankiaroot infection as well as in response to bacterial diffusible signals

(2015) Fernando Clavijo et al.   NEW PHYTOLOGIST

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Deep Sequencing of theMedicago truncatulaRoot Transcriptome Reveals a Massive and Early Interaction between Nodulation Factor and Ethylene Signals

(2015) Estíbaliz Larrainzar et al.   PLANT PHYSIOLOGY

Candidatus Frankia Datiscae Dg1, the Actinobacterial Microsymbiont of Datisca glomerata, Expresses the Canonical nod Genes nodABC in Symbiosis with Its Host Plant

(2015) Tomas Persson et al.   PLoS One

Large-scale phylogenetic analyses reveal multiple gains of actinorhizal nitrogen-fixing symbioses in angiosperms associated with climate change

(2015) Hong-Lei Li et al.   Scientific Reports

Does plant immunity play a critical role during initiation of the legume-rhizobium symbiosis?

(2015) Katalin Tóth et al.   Frontiers in Plant Science

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

NODULE INCEPTION Antagonistically Regulates Gene Expression with Nitrate in Lotus japonicus

(2014) Takashi Soyano et al.   PLANT AND CELL PHYSIOLOGY

An integrated analysis of plant and bacterial gene expression in symbiotic root nodules using laser-capture microdissection coupled to RNA sequencing

(2014) Brice Roux et al.   PLANT JOURNAL

Strigolactone Involvement in Root Development, Response to Abiotic Stress, and Interactions with the Biotic Soil Environment

(2014) Y. Kapulnik et al.   PLANT PHYSIOLOGY

A single evolutionary innovation drives the deep evolution of symbiotic N2-fixation in angiosperms

(2014) Gijsbert D. A. Werner et al.   Nature Communications

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Speak, friend and enter: signalling systems that promote beneficial symbiotic associations in plants

(2013) Giles E. D. Oldroyd   NATURE REVIEWS MICROBIOLOGY

The global nitrogen cycle in the twenty-first century

(2013) D. Fowler et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Independent Acquisition of Plant Root Nitrogen-Fixing Symbiosis in Fabids Recruited the Same Genetic Pathway for Nodule Organogenesis

(2013) Sergio Svistoonoff et al.   PLoS One

Comparison of the Nodule vs. Root Transcriptome of the Actinorhizal Plant Datisca glomerata: Actinorhizal Nodules Contain a Specific Class of Defensins

(2013) Irina V. Demina et al.   PLoS One

Allele Identification for Transcriptome-Based Population Genomics in the Invasive Plant Centaurea solstitialis

(2013) Katrina M. Dlugosch et al.   G3-Genes Genomes Genetics

Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction

(2012) Jian Ye et al.   BMC BIOINFORMATICS

Specialisation within the DWARF14 protein family confers distinct responses to karrikins and strigolactones in Arabidopsis

(2012) M. T. Waters et al.   DEVELOPMENT

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Nitric oxide (NO): a key player in the senescence of Medicago truncatula root nodules

(2012) Yvan Cam et al.   NEW PHYTOLOGIST

Arabidopsis histidine kinase 5 regulates salt sensitivity and resistance against bacterial and fungal infection

(2012) Jasmine Pham et al.   NEW PHYTOLOGIST

The diversity of actinorhizal symbiosis

(2012) Katharina Pawlowski et al.   PROTOPLASMA

The biology of strigolactones

(2012) Carolien Ruyter-Spira et al.   TRENDS IN PLANT SCIENCE

Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs

(2012) Adrian M. Altenhoff et al.   PLoS Computational Biology

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Phylogenetic Perspectives on the Origins of Nodulation

(2011) Jeff J. Doyle   MOLECULAR PLANT-MICROBE INTERACTIONS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Phytozome: a comparative platform for green plant genomics

(2011) David M. Goodstein et al.   NUCLEIC ACIDS RESEARCH

Transcriptomics of Actinorhizal Symbioses Reveals Homologs of the Whole Common Symbiotic Signaling Cascade

(2011) V. Hocher et al.   PLANT PHYSIOLOGY

Glutamine Synthetase Is a Molecular Target of Nitric Oxide in Root Nodules of Medicago truncatula and Is Regulated by Tyrosine Nitration

(2011) P. M. Melo et al.   PLANT PHYSIOLOGY

Strigolactones promote nodulation in pea

(2011) Eloise Foo et al.   PLANTA

The age and diversification of the angiosperms re-revisited

(2010) Charles D. Bell et al.   AMERICAN JOURNAL OF BOTANY

How Many Peas in a Pod? Legume Genes Responsible for Mutualistic Symbioses Underground

(2010) H. Kouchi et al.   PLANT AND CELL PHYSIOLOGY

The Arabidopsis Nitrate Transporter NRT1.8 Functions in Nitrate Removal from the Xylem Sap and Mediates Cadmium Tolerance

(2010) J.-Y. Li et al.   PLANT CELL

Polyploidy Did Not Predate the Evolution of Nodulation in All Legumes

(2010) Steven B. Cannon et al.   PLoS One

A remorin protein interacts with symbiotic receptors and regulates bacterial infection

(2010) B. Lefebvre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome Structure of the Legume, Lotus japonicus

(2008) S. Sato et al.   DNA RESEARCH

Strigolactone inhibition of shoot branching

(2008) Victoria Gomez-Roldan et al.   NATURE

Global inputs of biological nitrogen fixation in agricultural systems

(2008) David F. Herridge et al.   PLANT AND SOIL

The Histidine Kinase AHK5 Integrates Endogenous and Environmental Signals in Arabidopsis Guard Cells

(2008) Radhika Desikan et al.   PLoS One

The RPG gene of Medicago truncatula controls Rhizobium-directed polar growth during infection

(2008) J.-F. Arrighi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional Adaptation of a Plant Receptor- Kinase Paved the Way for the Evolution of Intracellular Root Symbioses with Bacteria

(2008) Katharina Markmann et al.   PLOS BIOLOGY