Comparative Genomics of a Plant-Parasitic Nematode Endosymbiont Suggest a Role in Nutritional Symbiosis

Nematode-Bacterium Symbioses—Cooperation and Conflict Revealed in the “Omics” Age

(2016) Kristen E. Murfin et al.   BIOLOGICAL BULLETIN

The Tiniest Tiny Genomes

(2014) Nancy A. Moran et al.   Annual Review of Microbiology

Prokka: rapid prokaryotic genome annotation

(2014) T. Seemann   BIOINFORMATICS

The Genome of Cardinium cBtQ1 Provides Insights into Genome Reduction, Symbiont Motility, and Its Settlement in Bemisia tabaci

(2014) Diego Santos-Garcia et al.   Genome Biology and Evolution

Small but Powerful, the Primary Endosymbiont of Moss Bugs, Candidatus Evansia muelleri, Holds a Reduced Genome with Large Biosynthetic Capabilities

(2014) Diego Santos-Garcia et al.   Genome Biology and Evolution

Swapping symbionts in spittlebugs: evolutionary replacement of a reduced genome symbiont

(2014) Ryuichi Koga et al.   ISME Journal

UniProt: a hub for protein information

(2014)   NUCLEIC ACIDS RESEARCH

Using Mitogenomic and Nuclear Ribosomal Sequence Data to Investigate the Phylogeny of the Xiphinema americanum Species Complex

(2014) Inga A. Zasada et al.   PLoS One

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

Palaeosymbiosis Revealed by Genomic Fossils of Wolbachia in a Strongyloidean Nematode

(2014) Georgios Koutsovoulos et al.   PLoS Genetics

Co-evolution between an Endosymbiont and Its Nematode Host: Wolbachia Asymmetric Posterior Localization and AP Polarity Establishment

(2014) Frederic Landmann et al.   PLoS Neglected Tropical Diseases

It Takes a Village: Ecological and Fitness Impacts of Multipartite Mutualism

(2013) Elizabeth A. Hussa et al.   Annual Review of Microbiology

A Paradigm for Endosymbiotic Life: Cell Differentiation ofRhizobiumBacteria Provoked by Host Plant Factors

(2013) Eva Kondorosi et al.   Annual Review of Microbiology

Draft genome sequence of the male-killing Wolbachia strain wBol1 reveals recent horizontal gene transfers from diverse sources

(2013) Anne Duplouy et al.   BMC GENOMICS

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

(2013) Filip Husnik et al.   CELL

Phylogenomics and Analysis of Shared Genes Suggest a Single Transition to Mutualism in Wolbachia of Nematodes

(2013) Francesco Comandatore et al.   Genome Biology and Evolution

Small, Smaller, Smallest: The Origins and Evolution of Ancient Dual Symbioses in a Phloem-Feeding Insect

(2013) Gordon M. Bennett et al.   Genome Biology and Evolution

Intranuclear verrucomicrobial symbionts and evidence of lateral gene transfer to the host protist in the termite gut

(2013) Tomoyuki Sato et al.   ISME Journal

Population genomics of a symbiont in the early stages of a pest invasion

(2013) Amanda M. V. Brown et al.   MOLECULAR ECOLOGY

The impact of microbial symbionts on host plant utilization by herbivorous insects

(2013) Allison K. Hansen et al.   MOLECULAR ECOLOGY

Top 10 plant-parasitic nematodes in molecular plant pathology

(2013) John T. Jones et al.   MOLECULAR PLANT PATHOLOGY

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases

(2013) Ron Caspi et al.   NUCLEIC ACIDS RESEARCH

Culture-Independent Investigation of the Microbiome Associated with the Nematode Acrobeloides maximus

(2013) Jean-Paul Baquiran et al.   PLoS One

Aphid amino acid transporter regulates glutamine supply to intracellular bacterial symbionts

(2013) D. R. G. Price et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Animals in a bacterial world, a new imperative for the life sciences

(2013) Margaret McFall-Ngai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cross-talk between Akkermansia muciniphila and intestinal epithelium controls diet-induced obesity

(2013) A. Everard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Widespread decay of vitamin-related pathways: coincidence or consequence?

(2013) Katherine E. Helliwell et al.   TRENDS IN GENETICS

Metagenomic De Novo Assembly of an Aquatic Representative of the Verrucomicrobial Class Spartobacteria

(2013) D. P. R. Herlemann et al.   mBio

Metagenomic analysis of the pinewood nematode microbiome reveals a symbiotic relationship critical for xenobiotics degradation

(2013) Xin-Yue Cheng et al.   Scientific Reports

A novel bacterial symbiont in the nematode Spirocerca lupi

(2012) Yuval Gottlieb et al.   BMC MICROBIOLOGY

Endosymbiosis

(2012) Jennifer J. Wernegreen   CURRENT BIOLOGY

Ecological interactions drive evolutionary loss of traits

(2012) Jacintha Ellers et al.   ECOLOGY LETTERS

Purifying Selection and Molecular Adaptation in the Genome of Verminephrobacter, the Heritable Symbiotic Bacteria of Earthworms

(2012) Kasper U. Kjeldsen et al.   Genome Biology and Evolution

A new type F Wolbachia from Splendidofilariinae (Onchocercidae) supports the recent emergence of this supergroup

(2012) Emilie Lefoulon et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

Complete Genome Sequence of “Candidatus Portiera aleyrodidarum” BT-QVLC, an Obligate Symbiont That Supplies Amino Acids and Carotenoids to Bemisia tabaci

(2012) Diego Santos-Garcia et al.   JOURNAL OF BACTERIOLOGY

The SAR11 Group of Alpha-Proteobacteria Is Not Related to the Origin of Mitochondria

(2012) Naiara Rodríguez-Ezpeleta et al.   PLoS One

Contribution of Lateral Gene Transfers to the Genome Composition and Parasitic Ability of Root-Knot Nematodes

(2012) Julien Paganini et al.   PLoS One

Toward almost closed genomes with GapFiller

(2012) Marten Boetzer et al.   GENOME BIOLOGY

New Clues about the Evolutionary History of Metabolic Losses in Bacterial Endosymbionts, Provided by the Genome of Buchnera aphidicola from the Aphid Cinara tujafilina

(2011) Araceli Lamelas et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Genomic and Physiological Characterization of the Verrucomicrobia Isolate Diplosphaera colitermitum gen. nov., sp. nov., Reveals Microaerophily and Nitrogen Fixation Genes

(2011) John T. Wertz et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data

(2011) T. Carver et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Purifying Selection, Sequence Composition, and Context-Specific Indel Mutations Shape Intraspecific Variation in a Bacterial Endosymbiont

(2011) Laura E. Williams et al.   Genome Biology and Evolution

Reductive Evolution of Bacterial Genome in Insect Gut Environment

(2011) Naruo Nikoh et al.   Genome Biology and Evolution

The power of paired genomes

(2011) NICOLE M. GERARDO et al.   MOLECULAR ECOLOGY

Genetic and metabolic determinants of nutritional phenotype in an insect-bacterial symbiosis

(2011) S. J. MACDONALD et al.   MOLECULAR ECOLOGY

Horizontal Gene Transfer in Nematodes: A Catalyst for Plant Parasitism?

(2011) Annelies Haegeman et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Bacterial symbionts in insects or the story of communities affecting communities

(2011) J. Ferrari et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Genome of Akkermansia muciniphila, a Dedicated Intestinal Mucin Degrader, and Its Use in Exploring Intestinal Metagenomes

(2011) Mark W. J. van Passel et al.   PLoS One

The Entomopathogenic Bacterial Endosymbionts Xenorhabdus and Photorhabdus: Convergent Lifestyles from Divergent Genomes

(2011) John M. Chaston et al.   PLoS One

The under-recognized dominance of Verrucomicrobia in soil bacterial communities

(2011) Gaddy T. Bergmann et al.   SOIL BIOLOGY & BIOCHEMISTRY

The Evolution of Host Specialization in the Vertebrate Gut Symbiont Lactobacillus reuteri

(2011) Steven A. Frese et al.   PLoS Genetics

Ecology of Plant and Free-Living Nematodes in Natural and Agricultural Soil

(2010) Deborah A. Neher   Annual Review of Phytopathology

Functional Convergence in Reduced Genomes of Bacterial Symbionts Spanning 200 My of Evolution

(2010) John P. McCutcheon et al.   Genome Biology and Evolution

Evolutionary microbial genomics: insights into bacterial host adaptation

(2010) Christina Toft et al.   NATURE REVIEWS GENETICS

A complex journey: transmission of microbial symbionts

(2010) Monika Bright et al.   NATURE REVIEWS MICROBIOLOGY

Endosymbiont DNA in Endobacteria-Free Filarial Nematodes Indicates Ancient Horizontal Genetic Transfer

(2010) Samantha N. McNulty et al.   PLoS One

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

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

Multiple lateral gene transfers and duplications have promoted plant parasitism ability in nematodes

(2010) Etienne G. J. Danchin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tablet--next generation sequence assembly visualization

(2009) I. Milne et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Evolution and diversity of Rickettsia bacteria

(2009) Lucy A Weinert et al.   BMC BIOLOGY

The microbial dimension in insect nutritional ecology

(2009) A. E. Douglas   FUNCTIONAL ECOLOGY

An endosymbiotic bacterium in a plant-parasitic nematode: Member of a new Wolbachia supergroup

(2009) Annelies Haegeman et al.   INTERNATIONAL JOURNAL FOR PARASITOLOGY

A phylogenetic tree of nematodes based on about 1200 full-length small subunit ribosomal DNA sequences

(2009) Hanny van Megen et al.   NEMATOLOGY

Convergent evolution of metabolic roles in bacterial co-symbionts of insects

(2009) J. P. McCutcheon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Wolbachia as a bacteriocyte-associated nutritional mutualist

(2009) T. Hosokawa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Dynamics and Time Scale of Ongoing Genomic Erosion in Symbiotic Bacteria

(2009) N. A. Moran et al.   SCIENCE

Molecular characterization of the symbionts associated with marine nematodes of the genusRobbea

(2009) Christoph Bayer et al.   Environmental Microbiology Reports

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

(2009) Marie Touchon et al.   PLoS Genetics

Evidence for Metabolic Provisioning by a Common Invertebrate Endosymbiont, Wolbachia pipientis, during Periods of Nutritional Stress

(2009) Jeremy C. Brownlie et al.   PLoS Pathogens

Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia

(2008) Shaobin Hou et al.   Biology Direct

Inherited intracellular ecosystem: symbiotic bacteria share bacteriocytes in whiteflies

(2008) Yuval Gottlieb et al.   FASEB JOURNAL

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

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

Genome Evolution of Wolbachia Strain wPip from the Culex pipiens Group

(2008) L. Klasson et al.   MOLECULAR BIOLOGY AND EVOLUTION

Wolbachia: master manipulators of invertebrate biology

(2008) John H. Werren et al.   NATURE REVIEWS MICROBIOLOGY