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

Ecological genomics of mutualism decline in nitrogen-fixing bacteria

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

Diversity patterns of R hizobiaceae communities inhabiting soils, root surfaces and nodules reveal a strong selection of rhizobial partners by legumes

(2015) Fabiola Miranda-Sánchez et al.   ENVIRONMENTAL MICROBIOLOGY

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

(2015) Shin Okazaki et al.   ISME Journal

Population Genomics Analysis of Legume Host Preference for Specific Rhizobial Genotypes in the Rhizobium leguminosarum bv. viciae Symbioses

(2015) Beatriz Jorrin et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Recombinant transfer in the basic genome ofEscherichia coli

(2015) Purushottam D. Dixit et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Inferring Speciation Processes from Patterns of Natural Variation in Microbial Genomes

(2015) David J. Krause et al.   SYSTEMATIC BIOLOGY

Eco-Evolutionary Dynamics of Episomes among Ecologically Cohesive Bacterial Populations

(2015) Hong Xue et al.   mBio

Microbial Speciation

(2015) B. Jesse Shapiro et al.   Cold Spring Harbor Perspectives in Biology

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

(2015) N. Kumar et al.   Open Biology

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

(2015) Xavier Didelot et al.   PLoS Computational Biology

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Explaining microbial genomic diversity in light of evolutionary ecology

(2014) Otto X. Cordero et al.   NATURE REVIEWS MICROBIOLOGY

Correction: A Common Genomic Framework for a Diverse Assembly of Plasmids in the Symbiotic Nitrogen Fixing Bacteria

(2014) Lisa C. Crossman et al.   PLoS One

Ordering microbial diversity into ecologically and genetically cohesive units

(2014) B. Jesse Shapiro et al.   TRENDS IN MICROBIOLOGY

Examination of Prokaryotic Multipartite Genome Evolution through Experimental Genome Reduction

(2014) George C. diCenzo et al.   PLoS Genetics

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

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

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

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

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 Early Events in the Ecological Differentiation of Bacteria

(2012) B. J. Shapiro et al.   SCIENCE

Rhizobium etli taxonomy revised with novel genomic data and analyses

(2012) Martha G. López-Guerrero et al.   SYSTEMATIC AND APPLIED MICROBIOLOGY

Plasmid-mediated horizontal gene transfer is a coevolutionary process

(2012) Ellie Harrison et al.   TRENDS IN MICROBIOLOGY

Patterns of Gene Flow Define Species of Thermophilic Archaea

(2012) Hinsby Cadillo-Quiroz et al.   PLOS BIOLOGY

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

(2012) Brendan Epstein et al.   PLoS Genetics

Genomic lineages of Rhizobium etli revealed by the extent of nucleotide polymorphisms and low recombination

(2011) José L Acosta et al.   BMC EVOLUTIONARY BIOLOGY

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

(2011) Xavier Bailly et al.   ISME Journal

Evolutionary Dynamics of Insertion Sequences in Relation to the Evolutionary Histories of the Chromosome and Symbiotic Plasmid Genes of Rhizobium etli Populations

(2010) L. Lozano et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Conserved Symbiotic Plasmid DNA Sequences in the Multireplicon Pangenomic Structure of Rhizobium etli

(2010) V. Gonzalez et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Mugsy: fast multiple alignment of closely related whole genomes

(2010) Samuel V. Angiuoli et al.   BIOINFORMATICS

pegas: an R package for population genetics with an integrated-modular approach

(2010) E. Paradis   BIOINFORMATICS

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

(2010) Murray P Cox et al.   BMC BIOINFORMATICS

Prodigal: prokaryotic gene recognition and translation initiation site identification

(2010) Doug Hyatt et al.   BMC BIOINFORMATICS

Alarming β-lactamase-mediated resistance in multidrug-resistant Enterobacteriaceae

(2010) Karen Bush   CURRENT OPINION IN MICROBIOLOGY

progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement

(2010) Aaron E. Darling et al.   PLoS One

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

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

Shifting the genomic gold standard for the prokaryotic species definition

(2009) Michael Richter et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity

(2009) C. Fraser et al.   SCIENCE

Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths

(2009) Marie Touchon et al.   PLoS Genetics

Coexistence of predominantly nonculturable rhizobia with diverse, endophytic bacterial taxa within nodules of wild legumes

(2008) Rosella Muresu et al.   FEMS MICROBIOLOGY ECOLOGY

Rhizobial secreted proteins as determinants of host specificity in the rhizobium–legume symbiosis

(2008) Maarten Fauvart et al.   FEMS MICROBIOLOGY LETTERS

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Recombination of synthetic oligonucleotides with prokaryotic chromosomes: substrate requirements of theEscherichia coli/λRed andSulfolobus acidocaldariusrecombination systems

(2008) Dennis W. Grogan et al.   MOLECULAR MICROBIOLOGY

Diversifying Selection and Concerted Evolution of a Type IV Secretion System in Bartonella

(2007) B. Nystedt et al.   MOLECULAR BIOLOGY AND EVOLUTION