Phylogenomics reveals multiple losses of nitrogen-fixing root nodule symbiosis

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(2018) Diep Thi Hoang et al.   BMC EVOLUTIONARY BIOLOGY

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

CRISPR/Cas9-Mediated Mutagenesis of Four Putative Symbiosis Genes of the Tropical Tree Parasponia andersonii Reveals Novel Phenotypes

(2018) Arjan van Zeijl et al.   Frontiers in Plant Science

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Biogeography of nodulated legumes and their nitrogen-fixing symbionts

(2017) Janet I. Sprent et al.   NEW PHYTOLOGIST

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

Transcriptome profiles reveal gene regulation of peanut (Arachis hypogaea L.) nodulation

(2017) Ze Peng et al.   Scientific Reports

Chasing unicorns: Nodulation origins and the paradox of novelty

(2016) Jeff J. Doyle   AMERICAN JOURNAL OF BOTANY

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution by gene loss

(2016) Ricard Albalat et al.   NATURE REVIEWS GENETICS

Are We There Yet? Reliably Estimating the Completeness of Plant Genome Sequences

(2016) Elisabeth Veeckman et al.   PLANT CELL

Root nodule symbiosis inLotus japonicusdrives the establishment of distinctive rhizosphere, root, and nodule bacterial communities

(2016) Rafal Zgadzaj et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Losing Complexity: The Role of Simplification in Macroevolution

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Tracing the evolutionary path to nitrogen-fixing crops

(2015) Pierre-Marc Delaux et al.   CURRENT OPINION IN PLANT BIOLOGY

FastME 2.0: A Comprehensive, Accurate, and Fast Distance-Based Phylogeny Inference Program: Table 1.

(2015) Vincent Lefort et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2015) Fernando Clavijo et al.   NEW PHYTOLOGIST

Convergent evolution of strigolactone perception enabled host detection in parasitic plants

(2015) C. E. Conn et al.   SCIENCE

Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference

(2015) Ge Tan et al.   SYSTEMATIC BIOLOGY

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

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

A novel bioinformatics pipeline to discover genes related to arbuscular mycorrhizal symbiosis based on their evolutionary conservation pattern among higher plants

(2014) Patrick Favre et al.   BMC PLANT BIOLOGY

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

(2014) Rei Kajitani et al.   GENOME RESEARCH

Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics

(2014) Ya Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

A reference genome for common bean and genome-wide analysis of dual domestications

(2014) Jeremy Schmutz et al.   NATURE GENETICS

Protocol: a simple method for extracting next-generation sequencing quality genomic DNA from recalcitrant plant species

(2014) Adam Healey et al.   Plant Methods

Evolutionary Dynamics of Nitrogen Fixation in the Legume–Rhizobia Symbiosis

(2014) Hironori Fujita et al.   PLoS One

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

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

Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts

(2014) László G. Nagy et al.   Nature Communications

Comparative Phylogenomics Uncovers the Impact of Symbiotic Associations on Host Genome Evolution

(2014) Pierre-Marc Delaux et al.   PLoS Genetics

GenomeTools: A Comprehensive Software Library for Efficient Processing of Structured Genome Annotations

(2013) Gordon Gremme et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Micromonospora is a normal occupant of actinorhizal nodules

(2013) Lorena Carro et al.   JOURNAL OF BIOSCIENCES

Estimating Gene Gain and Loss Rates in the Presence of Error in Genome Assembly and Annotation Using CAFE 3

(2013) Mira V. Han et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

The genetic causes of convergent evolution

(2013) David L. Stern   NATURE REVIEWS GENETICS

Evolution of a symbiotic receptor through gene duplications in the legume-rhizobium mutualism

(2013) Stéphane De Mita et al.   NEW PHYTOLOGIST

MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations

(2013) M. S. Campbell et al.   PLANT PHYSIOLOGY

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

Distribution of nitrogen fixation and nitrogenase-like sequences amongst microbial genomes

(2012) Patricia C Dos Santos et al.   BMC GENOMICS

Molecular characterization of the Lotus japonicus NRT1(PTR) and NRT2 families

(2012) GIUSEPPINA CRISCUOLO et al.   PLANT CELL AND ENVIRONMENT

Evaluating Methods for Isolating Total RNA and Predicting the Success of Sequencing Phylogenetically Diverse Plant Transcriptomes

(2012) Marc T. J. Johnson et al.   PLoS One

Phylogenomics and a posteriori data partitioning resolve the Cretaceous angiosperm radiation Malpighiales

(2012) Z. Xi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The diversity of actinorhizal symbiosis

(2012) Katharina Pawlowski et al.   PROTOPLASMA

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Phylogenetic Perspectives on the Origins of Nodulation

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

The Medicago genome provides insight into the evolution of rhizobial symbioses

(2011) Nevin D. Young et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Future Prospects for Cereals That Fix Nitrogen

(2011) P. H. Beatty et al.   SCIENCE

The age and diversification of the angiosperms re-revisited

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

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences

(2010) Y. Han et al.   NUCLEIC ACIDS RESEARCH

The Medicago truncatula gene expression atlas web server

(2009) Ji He et al.   BMC BIOINFORMATICS

Deep homology and the origins of evolutionary novelty

(2009) Neil Shubin et al.   NATURE

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

(2008) Sean B. Carroll   CELL

NITROGEN LIMITATION OF NET PRIMARY PRODUCTIVITY IN TERRESTRIAL ECOSYSTEMS IS GLOBALLY DISTRIBUTED

(2008) David S. LeBauer et al.   ECOLOGY

Arbuscular mycorrhiza: the mother of plant root endosymbioses

(2008) Martin Parniske   NATURE REVIEWS MICROBIOLOGY

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

SymRK defines a common genetic basis for plant root endosymbioses with arbuscular mycorrhiza fungi, rhizobia, and Frankiabacteria

(2008) H. Gherbi 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