Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex

Global-level population genomics reveals differential effects of geography and phylogeny on horizontal gene transfer in soil bacteria

(2019) Alex Greenlon 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

High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries

(2018) Chirag Jain et al.   Nature Communications

Adaptive evolution of rhizobial symbiotic compatibility mediated by co-evolved insertion sequences

(2017) Ran Zhao et al.   ISME Journal

Forms of natural selection controlling the genomic evolution in nodule bacteria

(2017) N. A. Provorov et al.   RUSSIAN JOURNAL OF GENETICS

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

Plant nodulation inducers enhance horizontal gene transfer ofAzorhizobium caulinodanssymbiosis island

(2016) Jun Ling et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Symbiosis within Symbiosis: Evolving Nitrogen-Fixing Legume Symbionts

(2016) Philippe Remigi et al.   TRENDS IN MICROBIOLOGY

Not So Simple After All: Bacteria, Their Population Genetics, and Recombination

(2016) William P. Hanage   Cold Spring Harbor Perspectives in Biology

TherepABCPlasmids with Quorum-Regulated Transfer Systems in Members of the Rhizobiales Divide into Two Structurally and Separately Evolving Groups

(2015) Margaret E. Wetzel et al.   Genome Biology and Evolution

Bacterial genospecies that are not ecologically coherent: population genomics of Rhizobium leguminosarum

(2015) N. Kumar et al.   Open Biology

Recent Selective Sweeps in North American Drosophila melanogaster Show Signatures of Soft Sweeps

(2015) Nandita R. Garud et al.   PLoS Genetics

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

Genomic Signature of Adaptation to Climate inMedicago truncatula

(2014) Jeremy B. Yoder et al.   GENETICS

Genome-Wide Association in Tomato Reveals 44 Candidate Loci for Fruit Metabolic Traits

(2014) C. Sauvage et al.   PLANT PHYSIOLOGY

Orthology Detection Combining Clustering and Synteny for Very Large Datasets

(2014) Marcus Lechner et al.   PLoS One

Genome-Wide Association Studies Identifies Seven Major Regions Responsible for Iron Deficiency Chlorosis in Soybean (Glycine max)

(2014) Sujan Mamidi et al.   PLoS One

QUAST: quality assessment tool for genome assemblies

(2013) Alexey Gurevich et al.   BIOINFORMATICS

Mantel test in population genetics

(2013) José Alexandre F. Diniz-Filho et al.   GENETICS AND MOLECULAR BIOLOGY

Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden

(2013) Quan Long et al.   NATURE GENETICS

Dismantling the Mantel tests

(2013) Gilles Guillot et al.   Methods in Ecology and Evolution

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Widespread fitness alignment in the legume-rhizobium symbiosis

(2012) Maren L. Friesen   NEW PHYTOLOGIST

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

The conjugative plasmid of a bean-nodulating Sinorhizobium fredii strain is assembled from sequences of two Rhizobium plasmids and the chromosome of a Sinorhizobium strain

(2011) Laura Cervantes et al.   BMC MICROBIOLOGY

Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness

(2011) B Mangin et al.   HEREDITY

Population genomics of Sinorhizobium medicae based on low-coverage sequencing of sympatric isolates

(2011) Xavier Bailly et al.   ISME Journal

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Symbiovars in rhizobia reflect bacterial adaptation to legumes

(2011) Marco A. Rogel et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

POOR STATISTICAL PERFORMANCE OF THE MANTEL TEST IN PHYLOGENETIC COMPARATIVE ANALYSES

(2010) Luke J. Harmon et al.   EVOLUTION

Introducing the bacterial ‘chromid’: not a chromosome, not a plasmid

(2010) Peter W. Harrison et al.   TRENDS IN MICROBIOLOGY

Efficient Methods to Compute Genomic Predictions

(2008) P.M. VanRaden   JOURNAL OF DAIRY SCIENCE