Coevolving Plasmids Drive Gene Flow and Genome Plasticity in Host-Associated Intracellular Bacteria

The Nature and Extent of Plasmid Variation in Chlamydia trachomatis

(2020) Charlotte A. Jones et al.   Microorganisms

Marine Sediments Illuminate Chlamydiae Diversity and Evolution

(2020) Jennah E. Dharamshi et al.   CURRENT BIOLOGY

Diversity in Chlamydial plasmids

(2020) Kolos V. Szabo et al.   PLoS One

Coevolution of host–plasmid pairs facilitates the emergence of novel multidrug resistance

(2020) Hannah Jordt et al.   Nature Ecology & Evolution

Chlamydiae in the Environment

(2020) Astrid Collingro et al.   TRENDS IN MICROBIOLOGY

Integrated mobile genetic elements in Thaumarchaeota

(2019) Mart Krupovic et al.   ENVIRONMENTAL MICROBIOLOGY

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Emergence of plasmid stability under non-selective conditions maintains antibiotic resistance

(2019) Tanita Wein et al.   Nature Communications

Chromosomal recombination targets in Chlamydia interspecies lateral gene transfer

(2019) Robert J. Suchland et al.   JOURNAL OF BACTERIOLOGY

Genomic analyses of the Chlamydia trachomatis core genome show an association between chromosomal genome, plasmid type and disease

(2018) Bart Versteeg et al.   BMC GENOMICS

Bipartite Network Analysis of Gene Sharings in the Microbial World

(2018) Eduardo Corel et al.   MOLECULAR BIOLOGY AND EVOLUTION

Toxins, Targets, and Triggers: An Overview of Toxin-Antitoxin Biology

(2018) Alexander Harms et al.   MOLECULAR CELL

Convergent Evolution in Intracellular Elements: Plasmids as Model Endosymbionts

(2018) Anne-Kathrin Dietel et al.   TRENDS IN MICROBIOLOGY

Plasmid Negative Regulation of CPAF Expression Is Pgp4 Independent and Restricted to Invasive Chlamydia trachomatis Biovars

(2018) Michael John Patton et al.   mBio

Temporal dynamics of bacteria-plasmid coevolution under antibiotic selection

(2018) Michael J. Bottery et al.   ISME Journal

Evolution of Plasmid-Mediated Antibiotic Resistance in the Clinical Context

(2018) Alvaro San Millan   TRENDS IN MICROBIOLOGY

The Genetic Transformation of Chlamydia pneumoniae

(2018) Kensuke Shima et al.   mSphere

Comprehensive global genome dynamics of Chlamydia trachomatis show ancient diversification followed by contemporary mixing and recent lineage expansion

(2017) James Hadfield et al.   GENOME RESEARCH

dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication

(2017) Matthew R Olm et al.   ISME Journal

Chance and necessity in the genome evolution of endosymbiotic bacteria of insects

(2017) Beatriz Sabater-Muñoz et al.   ISME Journal

Primates, Lice and Bacteria: Speciation and Genome Evolution in the Symbionts of Hominid Lice

(2017) Bret M. Boyd et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

UFBoot2: Improving the Ultrafast Bootstrap Approximation

(2017) Diep Thi Hoang et al.   MOLECULAR BIOLOGY AND EVOLUTION

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Modeling Site Heterogeneity with Posterior Mean Site Frequency Profiles Accelerates Accurate Phylogenomic Estimation

(2017) Huai-Chun Wang et al.   SYSTEMATIC BIOLOGY

Chlamydial Plasmid-Dependent Pathogenicity

(2017) Guangming Zhong   TRENDS IN MICROBIOLOGY

Developmental Cycle and Genome Analysis of Protochlamydia massiliensis sp. nov. a New Species in the Parachlamydiacae Family

(2017) Samia Benamar et al.   Frontiers in Cellular and Infection Microbiology

Adaptive modulation of antibiotic resistance through intragenomic coevolution

(2017) Michael J. Bottery et al.   Nature Ecology & Evolution

Positive selection inhibits gene mobilization and transfer in soil bacterial communities

(2017) James P. J. Hall et al.   Nature Ecology & Evolution

The cryptic plasmid is more important for Chlamydia muridarum to colonize the mouse gastrointestinal tract than to infect the genital tract

(2017) Lili Shao et al.   PLoS One

Emerging patterns of plasmid-host coevolution that stabilize antibiotic resistance

(2017) Thibault Stalder et al.   Scientific Reports

ecceTERA: comprehensive gene tree-species tree reconciliation using parsimony: Table 1.

(2016) Edwin Jacox et al.   BIOINFORMATICS

CRISPR System Acquisition and Evolution of an Obligate IntracellularChlamydia-Related Bacterium

(2016) Claire Bertelli et al.   Genome Biology and Evolution

Survival and Evolution of a Large Multidrug Resistance Plasmid in New Clinical Bacterial Hosts

(2016) Andreas Porse et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolved plasmid-host interactions reduce plasmid interference cost

(2016) Hirokazu Yano et al.   MOLECULAR MICROBIOLOGY

Source–sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities

(2016) James P. J. Hall et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Asexual Amoebae Escape Muller's Ratchet through Polyploidy

(2016) Sutherland K. Maciver   TRENDS IN PARASITOLOGY

Defying Muller’s Ratchet: Ancient Heritable Endobacteria Escape Extinction through Retention of Recombination and Genome Plasticity

(2016) Mizue Naito et al.   mBio

Developmental Cycle and Genome Analysis of “Rubidus massiliensis,” a New Vermamoeba vermiformis Pathogen

(2016) Jacques Y. Bou Khalil et al.   Frontiers in Cellular and Infection Microbiology

A fast method for calculating reliable event supports in tree reconciliations via Pareto optimality

(2015) Thu-Hien To et al.   BMC BIOINFORMATICS

Plasmids are vectors for redundant chromosomal genes in the Bacillus cereus group

(2015) Jinshui Zheng et al.   BMC GENOMICS

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

(2015) Donovan H. Parks et al.   GENOME RESEARCH

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

GenBank

(2015) Karen Clark et al.   NUCLEIC ACIDS RESEARCH

Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

(2015) Nuala A. O'Leary et al.   NUCLEIC ACIDS RESEARCH

Viral dark matter and virus–host interactions resolved from publicly available microbial genomes

(2015) Simon Roux et al.   eLife

Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights

(2015) Claire Bertelli et al.   Frontiers in Microbiology

Genomics of microbial plasmids: classification and identification based on replication and transfer systems and host taxonomy

(2015) Masaki Shintani et al.   Frontiers in Microbiology

Joint amalgamation of most parsimonious reconciled gene trees

(2014) Celine Scornavacca et al.   BIOINFORMATICS

Plasmid-Encoded Pgp3 Is a Major Virulence Factor for Chlamydia muridarum To Induce Hydrosalpinx in Mice

(2014) Yuanjun Liu et al.   INFECTION AND IMMUNITY

Positive selection and compensatory adaptation interact to stabilize non-transmissible plasmids

(2014) A. San Millan et al.   Nature Communications

Evolution and dynamics of megaplasmids with genome sizes larger than 100 kb in the Bacillus cereus group

(2013) Jinshui Zheng et al.   BMC EVOLUTIONARY BIOLOGY

Chlamydia trachomatis Plasmid-Encoded Pgp4 Is a Transcriptional Regulator of Virulence-Associated Genes

(2013) Lihua Song et al.   INFECTION AND IMMUNITY

Characterization of Chlamydia trachomatis Plasmid-Encoded Open Reading Frames

(2013) S. Gong et al.   JOURNAL OF BACTERIOLOGY

Assessment of the load and transcriptional dynamics of Chlamydia trachomatis plasmid according to strains’ tissue tropism

(2013) Rita Ferreira et al.   MICROBIOLOGICAL RESEARCH

Ultrafast Approximation for Phylogenetic Bootstrap

(2013) B. Q. Minh et al.   MOLECULAR BIOLOGY AND EVOLUTION

PhyloBayes MPI: Phylogenetic Reconstruction with Infinite Mixtures of Profiles in a Parallel Environment

(2013) Nicolas Lartillot et al.   SYSTEMATIC BIOLOGY

Horizontal Gene Transfer Can Rescue Prokaryotes from Muller’s Ratchet: Benefit of DNA from Dead Cells and Population Subdivision

(2013) Nobuto Takeuchi et al.   G3-Genes Genomes Genetics

Analysis of Genome Content Evolution in PVC Bacterial Super-Phylum: Assessment of Candidate Genes Associated with Cellular Organization and Lifestyle

(2012) Olga K. Kamneva et al.   Genome Biology and Evolution

Detecting overlapping protein complexes in protein-protein interaction networks

(2012) Tamás Nepusz et al.   NATURE METHODS

Plasmid-mediated horizontal gene transfer is a coevolutionary process

(2012) Ellie Harrison et al.   TRENDS IN MICROBIOLOGY

Unraveling the basic biology and clinical significance of the chlamydial plasmid: Figure 1.

(2011) Daniel D. Rockey   JOURNAL OF EXPERIMENTAL MEDICINE

A live-attenuated chlamydial vaccine protects against trachoma in nonhuman primates

(2011) Laszlo Kari et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Unity in Variety--The Pan-Genome of the Chlamydiae

(2011) A. Collingro et al.   MOLECULAR BIOLOGY AND EVOLUTION

Extreme genome reduction in symbiotic bacteria

(2011) John P. McCutcheon et al.   NATURE REVIEWS MICROBIOLOGY

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

Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes

(2011) Todd J. Treangen et al.   PLoS Genetics

Infectivity Acts asIn VivoSelection for Maintenance of the Chlamydial Cryptic Plasmid

(2010) Marsha Russell et al.   INFECTION AND IMMUNITY

Predicting Plasmid Promiscuity Based on Genomic Signature

(2010) H. Suzuki et al.   JOURNAL OF BACTERIOLOGY

Mobility of Plasmids

(2010) C. Smillie et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Rapid evolutionary innovation during an Archaean genetic expansion

(2010) Lawrence A. David et al.   NATURE

The Waddlia Genome: A Window into Chlamydial Biology

(2010) Claire Bertelli et al.   PLoS One

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

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

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

PhyloBayes 3: a Bayesian software package for phylogenetic reconstruction and molecular dating

(2009) Nicolas Lartillot et al.   BIOINFORMATICS

Co-evolution of genomes and plasmids within Chlamydia trachomatis and the emergence in Sweden of a new variant strain

(2009) Helena MB Seth-Smith et al.   BMC GENOMICS

Pathogenomics of the Virulence Plasmids of Escherichia coli

(2009) T. J. Johnson et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome

(2009) Marco Albrecht et al.   NUCLEIC ACIDS RESEARCH

Movement and equipositioning of plasmids by ParA filament disassembly

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

Noisy: Identification of problematic columns in multiple sequence alignments

(2008) Andreas WM Dress et al.   Algorithms for Molecular Biology

Chlamydiae as Symbionts in Eukaryotes

(2008) Matthias Horn   Annual Review of Microbiology

Empirical profile mixture models for phylogenetic reconstruction

(2008) Le Si Quang et al.   BIOINFORMATICS

The Whole-genome Sequencing of the Obligate Intracellular Bacterium Orientia tsutsugamushi Revealed Massive Gene Amplification During Reductive Genome Evolution

(2008) K. Nakayama et al.   DNA RESEARCH

The Chlamydia trachomatis Plasmid Is a Transcriptional Regulator of Chromosomal Genes and a Virulence Factor

(2008) J. H. Carlson et al.   INFECTION AND IMMUNITY

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

Using Mahalanobis distance to compare genomic signatures between bacterial plasmids and chromosomes

(2008) Haruo Suzuki et al.   NUCLEIC ACIDS RESEARCH