Comparative analysis of integrative and conjugative mobile genetic elements in the genus Mesorhizobium

Symbiosis islands of Loteae-nodulating Mesorhizobium comprise three radiating lineages with concordant nod gene complements and nodulation host-range groupings

(2020) Benjamin J. Perry et al.   Microbial Genomics

Evolution of diverse effective N2-fixing microsymbionts of Cicer arietinum following horizontal transfer of the Mesorhizobium ciceri CC1192 symbiosis integrative and conjugative element

(2020) Yvette Hill et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Minimal standards for the description of new genera and species of rhizobia and agrobacteria

(2019) Philippe M. de Lajudie et al.   INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

Exploring the evolutionary dynamics of Rhizobium plasmids through bipartite network analysis

(2019) Xiangchen Li et al.   ENVIRONMENTAL MICROBIOLOGY

Delineation of the integrase-attachment and origin-of-transfer regions of the symbiosis island ICEMlSymR7A

(2019) Callum J. Verdonk et al.   PLASMID

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

ape 5.0: an environment for modern phylogenetics and evolutionary analyses in R

(2018) Emmanuel Paradis et al.   BIOINFORMATICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Host Range and Genetic Plasticity Explain the Coexistence of Integrative and Extrachromosomal Mobile Genetic Elements

(2018) Jean Cury et al.   MOLECULAR BIOLOGY AND EVOLUTION

BAGEL4: a user-friendly web server to thoroughly mine RiPPs and bacteriocins

(2018) Auke J van Heel et al.   NUCLEIC ACIDS RESEARCH

Sequential induction of three recombination directionality factors directs assembly of tripartite integrative and conjugative elements

(2018) Timothy L. Haskett et al.   PLoS Genetics

Variation in bradyrhizobial NopP effector determines symbiotic incompatibility with Rj2-soybeans via effector-triggered immunity

(2018) Masayuki Sugawara et al.   Nature Communications

Complete genome sequence of the Robinia pseudoacacia L. symbiont Mesorhizobium amorphae CCNWGS0123

(2018) Xinye Wang et al.   Standards in Genomic Sciences

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

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

(2018) Chirag Jain et al.   Nature Communications

Evolution of copper resistance in the kiwifruit pathogenPseudomonas syringaepv.actinidiaethrough acquisition of integrative conjugative elements and plasmids

(2017) Elena Colombi et al.   ENVIRONMENTAL MICROBIOLOGY

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

The Obscure World of Integrative and Mobilizable Elements, Highly Widespread Elements that Pirate Bacterial Conjugative Systems

(2017) et al.   Genes

CRISPRDetect: A flexible algorithm to define CRISPR arrays

(2016) Ambarish Biswas et al.   BMC GENOMICS

“Every Gene Is Everywhere but the Environment Selects”: Global Geolocalization of Gene Sharing in Environmental Samples through Network Analysis

(2016) Marco Fondi et al.   Genome Biology and Evolution

PHASTER: a better, faster version of the PHAST phage search tool

(2016) David Arndt et al.   NUCLEIC ACIDS RESEARCH

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

Identification of protein secretion systems in bacterial genomes

(2016) Sophie S. Abby et al.   Scientific Reports

Integrative and Conjugative Elements (ICEs): What They Do and How They Work

(2015) Christopher M. Johnson et al.   Annual Review of Genetics

Roary: rapid large-scale prokaryote pan genome analysis

(2015) Andrew J. Page et al.   BIOINFORMATICS

An updated evolutionary classification of CRISPR–Cas systems

(2015) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

Ribosomal frameshifting and dual-target antiactivation restrict quorum-sensing–activated transfer of a mobile genetic element

(2015) Joshua P. Ramsay et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

(2015) Xavier Didelot et al.   PLoS Computational Biology

Genome sequence of the Lotus corniculatus microsymbiont Mesorhizobium loti strain R88B

(2015) Wayne Reeve et al.   Standards in Genomic Sciences

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Inter-phylum HGT has shaped the metabolism of many mesophilic and anaerobic bacteria

(2014) Alejandro Caro-Quintero et al.   ISME Journal

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

nhmmer: DNA homology search with profile HMMs

(2013) T. J. Wheeler et al.   BIOINFORMATICS

Legume growth-promoting rhizobia: An overview on the Mesorhizobium genus

(2013) Marta Laranjo et al.   MICROBIOLOGICAL RESEARCH

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

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

The NifA-RpoN Regulon of Mesorhizobium loti Strain R7A and Its Symbiotic Activation by a Novel LacI/GalR-Family Regulator

(2013) John T. Sullivan et al.   PLoS One

Queuosine Biosynthesis Is Required for Sinorhizobium meliloti-Induced Cytoskeletal Modifications on HeLa Cells and Symbiosis with Medicago truncatula

(2013) Marta Marchetti et al.   PLoS One

CRISPRTarget

(2013) Ambarish Biswas et al.   RNA Biology

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

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

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

A widely conserved molecular switch controls quorum sensing and symbiosis island transfer inMesorhizobium lotithrough expression of a novel antiactivator

(2012) Joshua P. Ramsay et al.   MOLECULAR MICROBIOLOGY

‘Ca. Liberibacter asiaticus’ Proteins Orthologous with pSymA-Encoded Proteins of Sinorhizobium meliloti: Hypothetical Roles in Plant Host Interaction

(2012) L. David Kuykendall et al.   PLoS One

Mining the Sinorhizobium meliloti Transportome to Develop FRET Biosensors for Sugars, Dicarboxylates and Cyclic Polyols

(2012) Alexandre Bourdès et al.   PLoS One

Alignment-free detection of local similarity among viral and bacterial genomes

(2011) Mirjana Domazet-Lošo et al.   BIOINFORMATICS

Proteinortho: Detection of (Co-)orthologs in large-scale analysis

(2011) Marcus Lechner et al.   BMC BIOINFORMATICS

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation

(2011) Julien Guglielmini et al.   PLoS Genetics

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

The Accessory Genome of Pseudomonas aeruginosa

(2010) V. L. Kung et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Networks of Gene Sharing among 329 Proteobacterial Genomes Reveal Differences in Lateral Gene Transfer Frequency at Different Phylogenetic Depths

(2010) T. Kloesges et al.   MOLECULAR BIOLOGY AND EVOLUTION

Integrative and conjugative elements: mosaic mobile genetic elements enabling dynamic lateral gene flow

(2010) Rachel A. F. Wozniak et al.   NATURE REVIEWS MICROBIOLOGY

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

A LuxRI-family regulatory system controls excision and transfer of theMesorhizobium lotistrain R7A symbiosis island by activating expression of two conserved hypothetical genes

(2009) Joshua P. Ramsay et al.   MOLECULAR MICROBIOLOGY

Network analyses structure genetic diversity in independent genetic worlds

(2009) S. Halary et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative ICE Genomics: Insights into the Evolution of the SXT/R391 Family of ICEs

(2009) Rachel A. F. Wozniak et al.   PLoS Genetics

A novel streptococcal integrative conjugative element involved in iron acquisition

(2008) Zoe Heather et al.   MOLECULAR MICROBIOLOGY

Expression of theBradyrhizobium japonicumType III Secretion System in Legume Nodules and Analysis of the Associatedttsbox Promoter

(2008) Susanne Zehner et al.   MOLECULAR PLANT-MICROBE INTERACTIONS