Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches

Culture-Facilitated Comparative Genomics of the Facultative Symbiont Hamiltonella defensa

(2018) Germain Chevignon et al.   Genome Biology and Evolution

Evolutionary loss and replacement of Buchnera, the obligate endosymbiont of aphids

(2018) Rebecca A. Chong et al.   ISME Journal

Genomic Insight into Symbiosis-Induced Insect Color Change by a Facultative Bacterial Endosymbiont, “ Candidatus Rickettsiella viridis”

(2018) Naruo Nikoh et al.   mBio

Happens in the best of subfamilies: establishment and repeated replacements of co-obligate secondary endosymbionts within Lachninae aphids

(2017) Alejandro Manzano-Marín et al.   ENVIRONMENTAL MICROBIOLOGY

Microbial strain-level population structure and genetic diversity from metagenomes

(2017) Duy Tin Truong et al.   GENOME RESEARCH

Culture of an aphid heritable symbiont demonstrates its direct role in defence against parasitoids

(2017) Jayce W. Brandt et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Diversity in symbiont consortia in the pea aphid complex is associated with large phenotypic variation in the insect host

(2016) Mélanie Leclair et al.   EVOLUTIONARY ECOLOGY

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

Buchnera has changed flatmate but the repeated replacement of co-obligate symbionts is not associated with the ecological expansions of their aphid hosts

(2016) A. S. Meseguer et al.   MOLECULAR ECOLOGY

How multi-partner endosymbioses function

(2016) Angela E. Douglas   NATURE REVIEWS MICROBIOLOGY

Holes in the Hologenome: Why Host-Microbe Symbioses Are Not Holobionts

(2016) Angela E. Douglas et al.   mBio

dendextend: an R package for visualizing, adjusting and comparing trees of hierarchical clustering

(2015) Tal Galili   BIOINFORMATICS

Insect life history and the evolution of bacterial mutualism

(2015) Lee M. Henry et al.   ECOLOGY LETTERS

Detection of low-abundance bacterial strains in metagenomic datasets by eigengenome partitioning

(2015) Brian Cleary et al.   NATURE BIOTECHNOLOGY

Experimental replacement of an obligate insect symbiont

(2015) Nancy A. Moran et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Host Biology in Light of the Microbiome: Ten Principles of Holobionts and Hologenomes

(2015) Seth R. Bordenstein et al.   PLOS BIOLOGY

Microbiomes: unifying animal and plant systems through the lens of community ecology theory

(2015) Natalie Christian et al.   Frontiers in Microbiology

The Road to Metagenomics: From Microbiology to DNA Sequencing Technologies and Bioinformatics

(2015) Alejandra Escobar-Zepeda et al.   Frontiers in Genetics

Bacterial Communities Associated with Host-Adapted Populations of Pea Aphids Revealed by Deep Sequencing of 16S Ribosomal DNA

(2015) Jean-Pierre Gauthier et al.   PLoS One

MindTheGap: integrated detection and assembly of short and long insertions

(2014) G. Rizk et al.   BIOINFORMATICS

Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance

(2014) Tae-Hyuk Ahn et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Whole-genome re-sequencing of non-model organisms: lessons from unmapped reads

(2014) A Gouin et al.   HEREDITY

Widespread infection and diverse infection patterns ofWolbachiain Chinese aphids

(2014) Zhe Wang et al.   Insect Science

Binning metagenomic contigs by coverage and composition

(2014) Johannes Alneberg et al.   NATURE METHODS

GroopM: an automated tool for the recovery of population genomes from related metagenomes

(2014) Michael Imelfort et al.   PeerJ

Horizontally Transmitted Symbionts and Host Colonization of Ecological Niches

(2013) Lee M. Henry et al.   CURRENT BIOLOGY

Pathoscope: Species identification and strain attribution with unassembled sequencing data

(2013) O. E. Francis et al.   GENOME RESEARCH

Uncovering symbiont-driven genetic diversity across North American pea aphids

(2013) Jacob A. Russell et al.   MOLECULAR ECOLOGY

The bacterial communities in plant phloem-sap-feeding insects

(2013) Xiangfeng Jing et al.   MOLECULAR ECOLOGY

Multi-Infections of Feminizing Wolbachia Strains in Natural Populations of the Terrestrial Isopod Armadillidium Vulgare

(2013) Victorien Valette et al.   PLoS One

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

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

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

Do diet and taxonomy influence insect gut bacterial communities?

(2012) D. R. Colman et al.   MOLECULAR ECOLOGY

Genome scans reveal candidate regions involved in the adaptation to host plant in the pea aphid complex

(2012) J. Jaquiéry et al.   MOLECULAR ECOLOGY

Metagenomic microbial community profiling using unique clade-specific marker genes

(2012) Nicola Segata et al.   NATURE METHODS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Massive Genomic Decay in Serratia symbiotica, a Recently Evolved Symbiont of Aphids

(2011) Gaelen R. Burke et al.   Genome Biology and Evolution

Genomic basis of endosymbiont-conferred protection against an insect parasitoid

(2011) A. K. Hansen et al.   GENOME RESEARCH

Jane: a new tool for the cophylogeny reconstruction problem

(2010) Chris Conow et al.   Algorithms for Molecular Biology

Evolutionary history of aphid-plant associations and their role in aphid diversification

(2010) Jean Peccoud et al.   COMPTES RENDUS BIOLOGIES

Genome Sequence of the Pea Aphid Acyrthosiphon pisum

(2010)   PLOS BIOLOGY

Facultative Symbionts in Aphids and the Horizontal Transfer of Ecologically Important Traits

(2009) Kerry M. Oliver et al.   Annual Review of Entomology

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

A fragile metabolic network adapted for cooperation in the symbiotic bacterium Buchnera aphidicola

(2009) Gavin H Thomas et al.   BMC Systems Biology

The mosaic genome structure of the Wolbachia wRi strain infecting Drosophila simulans

(2009) L. Klasson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A continuum of genetic divergence from sympatric host races to species in the pea aphid complex

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

Hamiltonella defensa, genome evolution of protective bacterial endosymbiont from pathogenic ancestors

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

Post-Pleistocene radiation of the pea aphid complex revealed by rapidly evolving endosymbionts

(2009) J. Peccoud 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

Genomics and Evolution of Heritable Bacterial Symbionts

(2008) Nancy A. Moran et al.   Annual Review of Genetics

Diverse Phage-Encoded Toxins in a Protective Insect Endosymbiont

(2008) P. H. Degnan et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Efficient computation of the phylogenetic likelihood function on multi-gene alignments and multi-core architectures

(2008) A. Stamatakis et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Fine-scale cospeciation between Brachycaudus and Buchnera aphidicola: bacterial genome helps define species and evolutionary relationships in aphids

(2008) E. Jousselin et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES