Genomic dissection of an extended phenotype: Oak galling by a cynipid gall wasp

A galling insect activates plant reproductive programs during gall development

(2019) Jack C. Schultz et al.   Scientific Reports

Transcriptome Analysis of Chinese Chestnut (Castanea mollissima Blume) in Response to Dryocosmus kuriphilus Yasumatsu Infestation

(2019) Cancan Zhu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Functional diversification of horizontally acquired glycoside hydrolase family 45 (GH45) proteins in Phytophaga beetles

(2019) André Busch et al.   BMC EVOLUTIONARY BIOLOGY

Pathways of DNA Transfer to Plants from Agrobacterium tumefaciens and Related Bacterial Species

(2019) Benoît Lacroix et al.   Annual Review of Phytopathology

Plant Proteins and Processes Targeted by Parasitic Nematode Effectors

(2019) Joffrey Mejias et al.   Frontiers in Plant Science

Gall Wasp Transcriptomes Unravel Potential Effectors Involved in Molecular Dialogues With Oak and Rose

(2019) Sébastien Cambier et al.   Frontiers in Physiology

OUP accepted manuscript

(2018)   BIOINFORMATICS

Fast Evolution and Lineage-Specific Gene Family Expansions of Aphid Salivary Effectors Driven by Interactions with Host-Plants

(2018) Hélène Boulain et al.   Genome Biology and Evolution

Rhizobia: from saprophytes to endosymbionts

(2018) Philip Poole et al.   NATURE REVIEWS MICROBIOLOGY

Multiple Nodulation Genes Are Up-Regulated During Establishment of Reniform Nematode Feeding Sites in Soybean

(2018) Nathan W. Redding et al.   PHYTOPATHOLOGY

Whole-genome data reveal the complex history of a diverse ecological community

(2018) Lynsey Bunnefeld et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cytokinin transfer by a free-living mirid to Nicotiana attenuata recapitulates a strategy of endophytic insects

(2018) Christoph Brütting et al.   eLife

Identification of an aldehyde oxidase involved in indole-3-acetic acid synthesis in Bombyx mori silk gland

(2018) Mami Takei et al.   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

Heritable phytohormone profiles of poplar genotypes vary in resistance to a galling aphid

(2018) Melanie JA Body et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Endogenous viruses of parasitic wasps: variations on a common theme

(2017) Jean-Michel Drezen et al.   Current Opinion in Virology

Insect-induced plant phenotypes: Revealing mechanisms through comparative genomics of galling insects and their hosts

(2016) Paul D. Nabity   AMERICAN JOURNAL OF BOTANY

Identification and functional analysis of secreted effectors from phytoparasitic nematodes

(2016) Sajid Rehman et al.   BMC MICROBIOLOGY

Avirulence gene mapping in the Hessian fly ( Mayetiola destructor ) reveals a protein phosphatase 2C effector gene family

(2016) Chaoyang Zhao et al.   JOURNAL OF INSECT PHYSIOLOGY

Insect-induced effects on plants and possible effectors used by galling and leaf-mining insects to manipulate their host-plant

(2016) David Giron et al.   JOURNAL OF INSECT PHYSIOLOGY

Plant development regulated by cytokinin sinks

(2016) Evelyne Zürcher et al.   SCIENCE

Modulation of Host Cell Biology by Plant Pathogenic Microbes

(2015) Ruth Le Fevre et al.   Annual Review of Cell and Developmental Biology

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

The transcriptional landscape of insect galls: psyllid (Hemiptera) gall formation in Hawaiian Metrosideros polymorpha (Myrtaceae)

(2015) Sebastian Bailey et al.   BMC GENOMICS

Impacts of local adaptation of forest trees on associations with herbivorous insects: implications for adaptive forest management

(2015) Frazer H. Sinclair et al.   Evolutionary Applications

Adaptive significance of gall formation for a gall-inducing aphids on Japanese elm trees

(2015) Mami Takei et al.   JOURNAL OF INSECT PHYSIOLOGY

Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies

(2015) Christophe Plomion et al.   Molecular Ecology Resources

Metatranscriptome Analysis of Fig Flowers Provides Insights into Potential Mechanisms for Mutualism Stability and Gall Induction

(2015) Ellen O. Martinson et al.   PLoS One

The Discovery, Distribution, and Evolution of Viruses Associated with Drosophila melanogaster

(2015) Claire L. Webster et al.   PLOS BIOLOGY

Phylogeny, Evolution and Classification of Gall Wasps: The Plot Thickens

(2015) Fredrik Ronquist et al.   PLoS One

An emerging example of tritrophic coevolution between flies (Diptera: Fergusoninidae) and nematodes (Nematoda: Neotylenchidae) on Myrtaceae host plants

(2014) Leigh A. Nelson et al.   BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

Leaf development and morphogenesis

(2014) M. Bar et al.   DEVELOPMENT

Horizontal gene transfer and functional diversification of plant cell wall degrading polygalacturonases: Key events in the evolution of herbivory in beetles

(2014) Roy Kirsch et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

Biosynthetic pathway of the phytohormone auxin in insects and screening of its inhibitors

(2014) Hiroyoshi Suzuki et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

Phytohormone Dynamics Associated with Gall Insects, and their Potential Role in the Evolution of the Gall-Inducing Habit

(2014) John F. Tooker et al.   JOURNAL OF CHEMICAL ECOLOGY

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

The roles of polyamines during the lifespan of plants: from development to stress

(2014) Antonio F. Tiburcio et al.   PLANTA

Avirulence Effector Discovery in a Plant Galling and Plant Parasitic Arthropod, the Hessian Fly (Mayetiola destructor)

(2014) Rajat Aggarwal et al.   PLoS One

Origin of plant auxin biosynthesis

(2014) Jipei Yue et al.   TRENDS IN PLANT SCIENCE

Plant immunity in plant–aphid interactions

(2014) Maëlle Jaouannet et al.   Frontiers in Plant Science

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

Phytohormones in Japanese Mugwort Gall Induction by a Gall-Inducing Gall Midge

(2013) Yuichiro TANAKA et al.   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

Likelihood-based inference of population history from low-coveragede novogenome assemblies

(2013) Jack Hearn et al.   MOLECULAR ECOLOGY

Mp10 and Mp42 from the Aphid SpeciesMyzus persicaeTrigger Plant Defenses inNicotiana benthamianaThrough Different Activities

(2013) Patricia A. Rodriguez et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Leaf-galling phylloxera on grapes reprograms host metabolism and morphology

(2013) P. D. Nabity et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genome of the mustard leaf beetle encodes two active xylanases originally acquired from bacteria through horizontal gene transfer

(2013) Y. Pauchet et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Symbiosis catalyses niche expansion and diversification

(2013) J. B. Joy   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Arabinogalactan proteins in root–microbe interactions

(2013) Eric Nguema-Ona et al.   TRENDS IN PLANT SCIENCE

Plant parasitic nematode effectors target host defense and nuclear functions to establish feeding cells

(2013) Michaëel Quentin et al.   Frontiers in Plant Science

Draft genome of the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major forest pest

(2013) Christopher I Keeling et al.   GENOME BIOLOGY

Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots

(2013) Sujai Kumar et al.   Frontiers in Genetics

Gall Midges (Hessian Flies) as Plant Pathogens

(2012) Jeff J. Stuart et al.   Annual Review of Phytopathology

Combining proteomics and transcriptome sequencing to identify active plant-cell-wall-degrading enzymes in a leaf beetle

(2012) Roy Kirsch et al.   BMC GENOMICS

Transcriptome and full-length cDNA resources for the mountain pine beetle, Dendroctonus ponderosae Hopkins, a major insect pest of pine forests

(2012) Christopher I. Keeling et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

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

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

Dual RNA-seq of pathogen and host

(2012) Alexander J. Westermann et al.   NATURE REVIEWS MICROBIOLOGY

Ethylene in vegetative development: a tale with a riddle

(2012) Filip Vandenbussche et al.   NEW PHYTOLOGIST

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

A Chimeric Arabinogalactan Protein Promotes Somatic Embryogenesis in Cotton Cell Culture

(2012) S. Poon et al.   PLANT PHYSIOLOGY

An insect-induced novel plant phenotype for sustaining social life in a closed system

(2012) Mayako Kutsukake et al.   Nature Communications

Discovery of a New Gall-Inducing Species in the Inquiline Tribe Synergini (Hymenoptera: Cynipidae): Inconsistent Implications From Biology and Morphology

(2011) Y. Abe et al.   ANNALS OF THE ENTOMOLOGICAL SOCIETY OF AMERICA

Effector proteins that modulate plant–insect interactions

(2011) Saskia A Hogenhout et al.   CURRENT OPINION IN PLANT BIOLOGY

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Hessian Fly-Associated Bacteria: Transmission, Essentiality, and Composition

(2011) Raman Bansal et al.   PLoS One

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Developing EPIC markers for chalcidoid Hymenoptera from EST and genomic data

(2010) KONRAD LOHSE et al.   Molecular Ecology Resources

Root-knot nematodes (Meloidogyne spp.) in Europe

(2010) Wim Wesemael et al.   NEMATOLOGY

Diversity of Beetle Genes Encoding Novel Plant Cell Wall Degrading Enzymes

(2010) Yannick Pauchet et al.   PLoS One

Plant green-island phenotype induced by leaf-miners is mediated by bacterial symbionts

(2010) W. Kaiser et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Analysis of Virion Structural Components Reveals Vestiges of the Ancestral Ichnovirus Genome

(2010) Anne-Nathalie Volkoff et al.   PLoS Pathogens

Genome-Wide Identification, Structure and Expression Studies, and Mutant Collection of 22 Early Nodulin-Like Protein Genes in Arabidopsis

(2009) Kiyoshi MASHIGUCHI et al.   BIOSCIENCE BIOTECHNOLOGY AND BIOCHEMISTRY

Insect chitinase and chitinase-like proteins

(2009) Yasuyuki Arakane et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Extraordinarily widespread and fantastically complex: comparative biology of endosymbiotic bacterial and fungal mutualists of insects

(2009) Cara M. Gibson et al.   ECOLOGY LETTERS

Calreticulin: conserved protein and diverse functions in plants

(2009) Xiao-Yun Jia et al.   PHYSIOLOGIA PLANTARUM

Polydnaviruses of Braconid Wasps Derive from an Ancestral Nudivirus

(2009) A. Bezier et al.   SCIENCE

Host Niches and Defensive Extended Phenotypes Structure Parasitoid Wasp Communities

(2009) Richard Bailey et al.   PLOS BIOLOGY

Influence of Seed Head–Attacking Biological Control Agents on Spotted Knapweed Reproductive Potential in Western Montana Over a 30-Year Period

(2008) Jim M. Story et al.   ENVIRONMENTAL ENTOMOLOGY

Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

(2008) Pierre Abad et al.   NATURE BIOTECHNOLOGY

Functional specialization among insect chitinase family genes revealed by RNA interference

(2008) Q. Zhu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA