Comparative genomics reveals high rates of horizontal transfer and strong purifying selection on rhizobial symbiosis genes

Recurrent mutualism breakdown events in a legume rhizobia metapopulation

(2020) Kelsey A. Gano-Cohen et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

GeneRax: A Tool for Species-Tree-Aware Maximum Likelihood-Based Gene  Family Tree Inference under Gene Duplication, Transfer, and Loss

(2020) Benoit Morel et al.   MOLECULAR BIOLOGY AND EVOLUTION

Select and resequence reveals relative fitness of bacteria in symbiotic and free-living environments

(2018) Liana T. Burghardt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Horizontal Transfer of Symbiosis Genes within and Between Rhizobial Genera: Occurrence and Importance

(2018) Mitchell Andrews et al.   Genes

Mutualists Stabilize the Coexistence of Congeneric Legumes

(2018) Andrew Siefert et al.   AMERICAN NATURALIST

Measuring phylogenetic signal between categorical traits and phylogenies

(2018) Rui Borges et al.   BIOINFORMATICS

More partners, more ranges: generalist legumes spread more easily around the globe

(2018) Tia L. Harrison et al.   Biology Letters

Genome-Wide Association Analyses in the Model Rhizobium Ensifer meliloti

(2018) Brendan Epstein et al.   mSphere

STRIDE: Species Tree Root Inference from Gene Duplication Events

(2017) David M Emms et al.   MOLECULAR BIOLOGY AND EVOLUTION

Invasive legumes can associate with many mutualists of native legumes, but usually do not

(2017) Kimberly J. La Pierre et al.   Ecology and Evolution

Population genomics of the symbiotic plasmids of sympatric nitrogen-fixing Rhizobium species associated with Phaseolus vulgaris

(2016) Olga M. Pérez Carrascal et al.   ENVIRONMENTAL MICROBIOLOGY

Assembly and transfer of tripartite integrative and conjugative genetic elements

(2016) Timothy L. Haskett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ecological genomics of mutualism decline in nitrogen-fixing bacteria

(2016) Christie R. Klinger et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Nodulation outer proteins: double-edged swords of symbiotic rhizobia

(2015) C. Staehelin et al.   BIOCHEMICAL JOURNAL

Epidemic Spread of Symbiotic and Non-Symbiotic Bradyrhizobium Genotypes Across California

(2015) A. C. Hollowell et al.   MICROBIAL ECOLOGY

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

(2015) Vincent Lefort 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

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Transport and Metabolism in Legume-Rhizobia Symbioses

(2013) Michael Udvardi et al.   Annual Review of Plant Biology

Selection, genome-wide fitness effects and evolutionary rates in the model legumeMedicago truncatula

(2013) Timothy Paape et al.   MOLECULAR ECOLOGY

Mutualistic Co-evolution of Type III Effector Genes in Sinorhizobium fredii and Bradyrhizobium japonicum

(2013) Jeffrey A. Kimbrel et al.   PLoS Pathogens

Legumes select symbiosis island sequence variants inBradyrhizobium

(2012) MATTHEW A. PARKER   MOLECULAR ECOLOGY

Comparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations

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

Population Genomics of the Facultatively Mutualistic Bacteria Sinorhizobium meliloti and S. medicae

(2012) Brendan Epstein et al.   PLoS Genetics

Molecular adaptation in flowering and symbiotic recognition pathways: insights from patterns of polymorphism in the legume Medicago truncatula

(2011) Stéphane De Mita et al.   BMC EVOLUTIONARY BIOLOGY

Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti

(2011) Marco Galardini et al.   BMC GENOMICS

New paradigms for the evolution of beneficial infections

(2011) Joel L. Sachs et al.   TRENDS IN ECOLOGY & EVOLUTION

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Why do bacteria engage in homologous recombination?

(2009) Michiel Vos   TRENDS IN MICROBIOLOGY

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

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

The impact of horizontal gene transfer in shaping operons and protein interaction networks – direct evidence of preferential attachment

(2008) Wagied Davids et al.   BMC EVOLUTIONARY BIOLOGY