Tremblaya phenacola PPER: an evolutionary beta-gammaproteobacterium collage

Dissecting genome reduction and trait loss in insect endosymbionts

(2016) Amparo Latorre et al.   Annals of the New York Academy of Sciences

Reinventing the Wheel and Making It Round Again: Evolutionary Convergence inBuchnera–SerratiaSymbiotic Consortia between the Distantly Related Lachninae AphidsTuberolachnus salignusandCinara cedri

(2016) Alejandro Manzano-Marín et al.   Genome Biology and Evolution

Convergent patterns in the evolution of mealybug symbioses involving different intrabacterial symbionts

(2016) Gitta Szabó et al.   ISME Journal

Repeated replacement of an intrabacterial symbiont in the tripartite nested mealybug symbiosis

(2016) Filip Husnik et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

(2016) Daniel H. Huson et al.   PLoS Computational Biology

Metabolic Complementation in Bacterial Communities: Necessary Conditions and Optimality

(2016) Matteo Mori et al.   Frontiers in Microbiology

Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes

(2016) Hsin-Hung Lin et al.   Scientific Reports

KEGG as a reference resource for gene and protein annotation

(2015) Minoru Kanehisa 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

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

Sympatric Speciation in a Bacterial Endosymbiont Results in Two Genomes with the Functionality of One

(2014) James T. Van Leuven et al.   CELL

Genome Degeneration and Adaptation in a Nascent Stage of Symbiosis

(2014) Kelly F. Oakeson et al.   Genome Biology and Evolution

The evolution of bacterial DNA base composition

(2014) Deepa Agashe et al.   JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION

Parallel Histories of Horizontal Gene Transfer Facilitated Extreme Reduction of Endosymbiont Genomes in Sap-Feeding Insects

(2014) Daniel B. Sloan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolutionary origin of insect-Wolbachia nutritional mutualism

(2014) N. Nikoh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mealybugs nested endosymbiosis: going into the ‘matryoshka’ system in Planococcus citri in depth

(2013) Sergio López-Madrigal et al.   BMC MICROBIOLOGY

Horizontal Gene Transfer from Diverse Bacteria to an Insect Genome Enables a Tripartite Nested Mealybug Symbiosis

(2013) Filip Husnik et al.   CELL

Defensive Bacteriome Symbiont with a Drastically Reduced Genome

(2013) Atsushi Nakabachi et al.   CURRENT BIOLOGY

PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome

(2013) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Horizontal Transfer of Entire Genomes via Mitochondrial Fusion in the Angiosperm Amborella

(2013) D. W. Rice et al.   SCIENCE

PhyloPhlAn is a new method for improved phylogenetic and taxonomic placement of microbes

(2013) Nicola Segata et al.   Nature Communications

Mealybugs with distinct endosymbiotic systems living on the same host plant

(2012) Ryuichi Koga et al.   FEMS MICROBIOLOGY ECOLOGY

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

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

Evolutionary relationships of flavobacterial and enterobacterial endosymbionts with their scale insect hosts (Hemiptera: Coccoidea)

(2012) M. Rosenblueth et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Genome Reduction and Co-evolution between the Primary and Secondary Bacterial Symbionts of Psyllids

(2012) Daniel B. Sloan et al.   MOLECULAR BIOLOGY AND EVOLUTION

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

EcoCyc: fusing model organism databases with systems biology

(2012) Ingrid M. Keseler et al.   NUCLEIC ACIDS RESEARCH

Molecular and Histological Characterization of Primary (Betaproteobacteria) and Secondary (Gammaproteobacteria) Endosymbionts of Three Mealybug Species

(2011) Laurence N. Gatehouse et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

An Interdependent Metabolic Patchwork in the Nested Symbiosis of Mealybugs

(2011) John P. McCutcheon et al.   CURRENT BIOLOGY

Complete Genome Sequence of "Candidatus Tremblaya princeps" Strain PCVAL, an Intriguing Translational Machine below the Living-Cell Status

(2011) S. Lopez-Madrigal et al.   JOURNAL OF BACTERIOLOGY

Serratia symbiotica from the Aphid Cinara cedri: A Missing Link from Facultative to Obligate Insect Endosymbiont

(2011) Araceli Lamelas et al.   PLoS Genetics

Evolutionary Relationships among Primary Endosymbionts of the Mealybug Subfamily Phenacoccinae (Hemiptera: Coccoidea: Pseudococcidae)

(2010) M. E. Gruwell et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

genoPlotR: comparative gene and genome visualization in R

(2010) L. Guy et al.   BIOINFORMATICS

Recombination and the maintenance of plant organelle genome stability

(2010) Alexandre Maréchal et al.   NEW PHYTOLOGIST

One Bacterial Cell, One Complete Genome

(2010) Tanja Woyke et al.   PLoS One

A subfamily-level classification of mealybugs (Hemiptera: Pseudococcidae) based on integrated molecular and morphological data

(2010) NATE B. HARDY et al.   SYSTEMATIC ENTOMOLOGY

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

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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

The Organization of the Bacterial Genome

(2008) Eduardo P.C. Rocha   Annual Review of Genetics

Infection Dynamics of Coexisting Beta- and Gammaproteobacteria in the Nested Endosymbiotic System of Mealybugs

(2008) M. Kono et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Artemis and ACT: viewing, annotating and comparing sequences stored in a relational database

(2008) Tim Carver et al.   BIOINFORMATICS

Long-Term Evolutionary Stability of Bacterial Endosymbiosis in Curculionoidea: Additional Evidence of Symbiont Replacement in the Dryophthoridae Family

(2008) Cyrille Conord et al.   MOLECULAR BIOLOGY AND EVOLUTION

Learning how to live together: genomic insights into prokaryote–animal symbioses

(2008) Andrés Moya et al.   NATURE REVIEWS GENETICS

Are biologists in 'future shock'? Symbiosis integrates biology across domains

(2008) Margaret McFall-Ngai   NATURE REVIEWS MICROBIOLOGY