Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum

A Novel RNA Virus in the Parasitoid Wasp Lysiphlebus fabarum: Genomic Structure, Prevalence, and Transmission

(2020) Martina N. Lüthi et al.   Viruses-Basel

Apollo: Democratizing genome annotation

(2019) Nathan A. Dunn et al.   PLoS Computational Biology

Functional crosstalk across IMD and Toll pathways: insight into the evolution of incomplete immune cascades

(2019) Yudai Nishide et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The preference‐performance relationship as a means of classifying parasitoids according to their specialization degree

(2019) Lucie S. Monticelli et al.   Evolutionary Applications

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

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

De novo gene birth

(2019) Stephen Branden Van Oss et al.   PLoS Genetics

OMA standalone: orthology inference among public and custom genomes and transcriptomes

(2019) Adrian M. Altenhoff et al.   GENOME RESEARCH

Gene Family Evolution in the Pea Aphid Based on Chromosome-Level Genome Assembly

(2019) Yiyuan Li et al.   MOLECULAR BIOLOGY AND EVOLUTION

How climate change affects the seasonal ecology of insect parasitoids

(2019) Kévin Tougeron et al.   ECOLOGICAL ENTOMOLOGY

Genome of the Parasitoid Wasp Diachasma alloeum, an Emerging Model for Ecological Speciation and Transitions to Asexual Reproduction

(2019) Eric S Tvedte et al.   Genome Biology and Evolution

DNA methylomes and transcriptomes analysis reveal implication of host DNA methylation machinery in BmNPV proliferation in Bombyx mori

(2019) Haoling Huang et al.   BMC GENOMICS

The genomes of two parasitic wasps that parasitize the diamondback moth

(2019) Min Shi et al.   BMC GENOMICS

Mapping of Multiple Complementary Sex Determination Loci in a Parasitoid Wasp

(2019) Cyril Matthey-Doret et al.   Genome Biology and Evolution

The role of defensive symbionts in host-parasite coevolution

(2018) Christoph Vorburger et al.   BIOLOGICAL REVIEWS

The genomic features of parasitism, Polyembryony and immune evasion in the endoparasitic wasp Macrocentrus cingulum

(2018) Chuanlin Yin et al.   BMC GENOMICS

Signatures of DNA Methylation across Insects Suggest Reduced DNA Methylation Levels in Holometabola

(2018) Panagiotis Provataris et al.   Genome Biology and Evolution

Conserved roles of Osiris genes in insect development, polymorphism and protection

(2018) C. R. Smith et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Codon Usage Bias in Animals: Disentangling the Effects of Natural Selection, Effective Population Size, and GC-Biased Gene Conversion

(2018) Nicolas Galtier et al.   MOLECULAR BIOLOGY AND EVOLUTION

Identifying Genomic Hotspots Of Differentiation And Candidate Genes Involved In The Adaptive Divergence Of Pea Aphid Host Races

(2018) Pierre Nouhaud et al.   MOLECULAR ECOLOGY

Genome Report: Whole Genome Sequence of the Parasitoid Wasp Microplitis demolitor That Harbors an Endogenous Virus Mutualist

(2018) Gaelen R. Burke et al.   G3-Genes Genomes Genetics

Quantifying the unquantifiable: why Hymenoptera, not Coleoptera, is the most speciose animal order

(2018) Andrew A. Forbes et al.   BMC ECOLOGY

Hemimetabolous genomes reveal molecular basis of termite eusociality

(2018) Mark C. Harrison et al.   Nature Ecology & Evolution

Replication-dependent histone isoforms: a new source of complexity in chromatin structure and function

(2018) Rajbir Singh et al.   NUCLEIC ACIDS RESEARCH

Systematics, Phylogeny, and Evolution of Braconid Wasps: 30 Years of Progress

(2018) Xue-xin Chen et al.   Annual Review of Entomology

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

The genome of the jellyfish Aurelia and the evolution of animal complexity

(2018) David A. Gold et al.   Nature Ecology & Evolution

Parasitoid gene expression changes after adaptation to symbiont-protected hosts

(2017) Alice B. Dennis et al.   EVOLUTION

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Maternal provision of non-sex-specific transformer messenger RNA in sex determination of the wasp Asobara tabida

(2017) E. Geuverink et al.   INSECT MOLECULAR BIOLOGY

Nine facultative endosymbionts in aphids. A review

(2017) Jianqing Guo et al.   JOURNAL OF ASIA-PACIFIC ENTOMOLOGY

SMS: Smart Model Selection in PhyML

(2017) Vincent Lefort et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genetic basis of octanoic acid resistance inDrosophila sechellia: functional analysis of a fine-mapped region

(2017) J. M. Andrade López et al.   MOLECULAR ECOLOGY

Male sex in houseflies is determined byMdmd, a paralog of the generic splice factor geneCWC22

(2017) Akash Sharma et al.   SCIENCE

Unraveling the venom components of an encyrtid endoparasitoid wasp Diversinervus elegans

(2017) Nai-Yong Liu et al.   TOXICON

Whole Genome Sequencing of the Braconid Parasitoid Wasp Fopius arisanus , an Important Biocontrol Agent of Pest Tepritid Fruit Flies

(2017) Scott M. Geib et al.   G3-Genes Genomes Genetics

Nine facultative endosymbionts in aphids. A review

(2017) Jianqing Guo et al.   JOURNAL OF ASIA-PACIFIC ENTOMOLOGY

Expression differences in Aphidius ervi (Hymenoptera: Braconidae) females reared on different aphid host species

(2017) Gabriel I. Ballesteros et al.   PeerJ

Identification and expression analysis of chemosensory receptor genes in an aphid endoparasitoid Aphidius gifuensis

(2017) Zhi-Wei Kang et al.   Scientific Reports

Evolution of genome size and genomic GC content in carnivorous holokinetics (Droseraceae)

(2016) Adam Veleba et al.   ANNALS OF BOTANY

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

Using intron position conservation for homology-based gene prediction

(2016) Jens Keilwagen et al.   NUCLEIC ACIDS RESEARCH

Are aphid parasitoids from mild winter climates losing their winter diapause?

(2016) Kévin Tougeron et al.   OECOLOGIA

Specificity of Multi-Modal Aphid Defenses against Two Rival Parasitoids

(2016) Adam J. Martinez et al.   PLoS One

The role of epigenetics in host–parasite coevolution: lessons from the model host insects Galleria mellonella and Tribolium castaneum

(2016) Andreas Vilcinskas   ZOOLOGY

Gene set of chemosensory receptors in the polyembryonic endoparasitoid Macrocentrus cingulum

(2016) Tofael Ahmed et al.   Scientific Reports

Seasonal phenotype-specific transcriptional reprogramming during metamorphosis in the European map butterflyAraschnia levana

(2016) Andreas Vilcinskas et al.   Ecology and Evolution

Comparative venomics of Psyttalia lounsburyi and P. concolor, two olive fruit fly parasitoids: a hypothetical role for a GH1 β-glucosidase

(2016) Hugo Mathé-Hubert et al.   Scientific Reports

Roles for Synonymous Codon Usage in Protein Biogenesis

(2015) Julie L. Chaney et al.   Annual Review of Biophysics

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Apolipophorin III from honeybees (Apis cerana) exhibits antibacterial activity

(2015) Bo Yeon Kim et al.   COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY B-BIOCHEMISTRY & MOLECULAR BIOLOGY

A Massive Expansion of Effector Genes Underlies Gall-Formation in the Wheat Pest Mayetiola destructor

(2015) Chaoyang Zhao et al.   CURRENT BIOLOGY

De Novo Assembly and Annotation of the Asian Tiger Mosquito (Aedes albopictus) Repeatome with dnaPipeTE from Raw Genomic Reads and Comparative Analysis with the Yellow Fever Mosquito (Aedes aegypti)

(2015) Clément Goubert et al.   Genome Biology and Evolution

Dissecting the contributions of GC content and codon usage to gene expression in the model algaChlamydomonas reinhardtii

(2015) Rouhollah Barahimipour et al.   PLANT JOURNAL

Are generalist Aphidiinae (Hym. Braconidae) mostly cryptic species complexes?

(2015) STEPHANE A. P. DEROCLES et al.   SYSTEMATIC ENTOMOLOGY

The iBeetle large-scale RNAi screen reveals gene functions for insect development and physiology

(2015) Christian Schmitt-Engel et al.   Nature Communications

Does sex-biased dispersal account for the lack of geographic and host-associated differentiation in introduced populations of an aphid parasitoid?

(2015) Francisca Zepeda-Paulo et al.   Ecology and Evolution

Evolutionary Consequences of DNA Methylation on the GC Content in Vertebrate Genomes

(2015) Carina F. Mugal et al.   G3-Genes Genomes Genetics

Venom Proteins from Parasitoid Wasps and Their Biological Functions

(2015) Sébastien Moreau et al.   Toxins

ALLMAPS: robust scaffold ordering based on multiple maps

(2015) Haibao Tang et al.   GENOME BIOLOGY

Repbase Update, a database of repetitive elements in eukaryotic genomes

(2015) Weidong Bao et al.   Mobile DNA

Impact of transposable elements on insect genomes and biology

(2015) Florian Maumus et al.   Current Opinion in Insect Science

proovread : large-scale high-accuracy PacBio correction through iterative short read consensus

(2014) Thomas Hackl et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information

(2014) Marten Boetzer et al.   BMC BIOINFORMATICS

Identification of the main venom protein components of Aphidius ervi, a parasitoid wasp of the aphid model Acyrthosiphon pisum

(2014) Dominique Colinet et al.   BMC GENOMICS

Convergent Genetic Architecture Underlies Social Organization in Ants

(2014) Jessica Purcell et al.   CURRENT BIOLOGY

EXPERIMENTAL EVOLUTION OF PARASITOID INFECTIVITY ON SYMBIONT-PROTECTED HOSTS LEADS TO THE EMERGENCE OF GENOTYPE SPECIFICITY

(2014) Romain Rouchet et al.   EVOLUTION

Efficient de novo assembly of highly heterozygous genomes from whole-genome shotgun short reads

(2014) Rei Kajitani et al.   GENOME RESEARCH

Exploring the hidden honeybee (Apis mellifera) venom proteome by integrating a combinatorial peptide ligand library approach with FTMS

(2014) Matthias Van Vaerenbergh et al.   Journal of Proteomics

Evolution of the Insect Desaturase Gene Family with an Emphasis on Social Hymenoptera

(2014) Martin Helmkampf et al.   MOLECULAR BIOLOGY AND EVOLUTION

Systematic analysis of a wasp parasitism arsenal

(2014) Gaelen R. Burke et al.   MOLECULAR ECOLOGY

PASTEC: An Automatic Transposable Element Classification Tool

(2014) Claire Hoede et al.   PLoS One

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Ecological and evolutionary significance of genomic GC content diversity in monocots

(2014) Petr Šmarda et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

New concepts in DNA methylation

(2014) Albert Jeltsch et al.   TRENDS IN BIOCHEMICAL SCIENCES

Teratocytes and their functions in parasitoids

(2014) Michael R Strand   Current Opinion in Insect Science

Insights into function and evolution of parasitoid wasp venoms

(2014) Marylène Poirié et al.   Current Opinion in Insect Science

nhmmer: DNA homology search with profile HMMs

(2013) T. J. Wheeler et al.   BIOINFORMATICS

NextClip: an analysis and read preparation tool for Nextera Long Mate Pair libraries

(2013) Richard M. Leggett et al.   BIOINFORMATICS

Adaptive evolution of a generalist parasitoid: implications for the effectiveness of biological control agents

(2013) Francisca A. Zepeda-Paulo et al.   Evolutionary Applications

Venom gland extract is not required for successful parasitism in the polydnavirus-associated endoparasitoid Hyposoter didymator (Hym. Ichneumonidae) despite the presence of numerous novel and conserved venom proteins

(2013) Tristan Dorémus et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Efficient translation initiation dictates codon usage at gene start

(2013) K. Bentele et al.   Molecular Systems Biology

A Y-like social chromosome causes alternative colony organization in fire ants

(2013) John Wang et al.   NATURE

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

(2013) Jaina Mistry et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

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

The diversity and fitness effects of infection with facultative endosymbionts in the grain aphid, Sitobion avenae

(2013) Piotr Łukasik et al.   OECOLOGIA

Epigenetic Regulation of Mouse Sex Determination by the Histone Demethylase Jmjd1a

(2013) S. Kuroki et al.   SCIENCE

Web Apollo: a web-based genomic annotation editing platform

(2013) Eduardo Lee et al.   GENOME BIOLOGY

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Codon usage bias: causative factors, quantification methods and genome-wide patterns: with emphasis on insect genomes

(2012) Susanta K. Behura et al.   BIOLOGICAL REVIEWS

Aphid parasitoids in biological control

(2012) Guy Boivin et al.   CANADIAN JOURNAL OF PLANT SCIENCE

Genome-wide association genetics of an adaptive trait in lodgepole pine

(2012) THOMAS L. PARCHMAN et al.   MOLECULAR ECOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Comparative studies of gene expression and the evolution of gene regulation

(2012) Irene Gallego Romero et al.   NATURE REVIEWS GENETICS

Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species

(2012) Brant K. Peterson et al.   PLoS One

The Cellular Immune Response of the Pea Aphid to Foreign Intrusion and Symbiotic Challenge

(2012) Antonin Schmitz et al.   PLoS One

Unique Features of Odorant-Binding Proteins of the Parasitoid Wasp Nasonia vitripennis Revealed by Genome Annotation and Comparative Analyses

(2012) Filipe G. Vieira et al.   PLoS One

Hyperparasitoids Use Herbivore-Induced Plant Volatiles to Locate Their Parasitoid Host

(2012) Erik H. Poelman et al.   PLOS BIOLOGY

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

A novel hybrid gene prediction method employing protein multiple sequence alignments

(2011) Oliver Keller et al.   BIOINFORMATICS

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

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Evolution of reproductive mode variation and host associations in a sexual-asexual complex of aphid parasitoids

(2011) Christoph Sandrock et al.   BMC EVOLUTIONARY BIOLOGY

New genome size estimates of 134 species of arthropods

(2011) Shawn Jason Hanrahan et al.   CHROMOSOME RESEARCH

Single-Locus Recessive Inheritance of Asexual Reproduction in a Parasitoid Wasp

(2011) Christoph Sandrock et al.   CURRENT BIOLOGY

Rapid evolution of parasitoids when faced with the symbiont-mediated resistance of their hosts

(2011) E. DION et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Considering Transposable Element Diversification in De Novo Annotation Approaches

(2011) Timothée Flutre et al.   PLoS One

Stacks : Building and Genotyping Loci De Novo From Short-Read Sequences

(2011) Julian M. Catchen et al.   G3-Genes Genomes Genetics

Comparative mitogenomics of Braconidae (Insecta: Hymenoptera) and the phylogenetic utility of mitochondrial genomes with special reference to Holometabolous insects

(2010) Shu-jun Wei et al.   BMC GENOMICS

Drosophila immune response: From systemic antimicrobial peptide production in fat body cells to local defense in the intestinal tract

(2010) Bernard Charroux et al.   FLY

Contrasting patterns of selective constraints in nuclear-encoded genes of the oxidative phosphorylation pathway in holometabolous insects and their possible role in hybrid breakdown in Nasonia

(2010) J D Gibson et al.   HEREDITY

An expansion of the genome size dataset for the insect order Hymenoptera, with a first test of parasitism and eusociality as possible constraints

(2010) A. M. Ardila-Garcia et al.   INSECT MOLECULAR BIOLOGY

The insect chemoreceptor superfamily of the parasitoid jewel waspNasonia vitripennis

(2010) H. M. Robertson et al.   INSECT MOLECULAR BIOLOGY

AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome

(2010) F. Legeai et al.   INSECT MOLECULAR BIOLOGY

Ant Mimicry by an Aphid Parasitoid,Lysiphlebus fabarum

(2010) Arash Rasekh et al.   JOURNAL OF INSECT SCIENCE

The Influence of Anticodon-Codon Interactions and Modified Bases on Codon Usage Bias in Bacteria

(2010) W. Ran et al.   MOLECULAR BIOLOGY AND EVOLUTION

Synonymous but not the same: the causes and consequences of codon bias

(2010) Joshua B. Plotkin et al.   NATURE REVIEWS GENETICS

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Comparative Genome Analysis Reveals an Absence of Leucine-Rich Repeat Pattern-Recognition Receptor Proteins in the Kingdom Fungi

(2010) Darren M. Soanes et al.   PLoS One

Functional and Evolutionary Insights from the Genomes of Three Parasitoid Nasonia Species

(2010) J. H. Werren et al.   SCIENCE

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

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Immunity and other defenses in pea aphids, Acyrthosiphon pisum

(2010) Nicole M Gerardo et al.   GENOME 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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Ecological Nitrogen Limitation Shapes the DNA Composition of Plant Genomes

(2009) C. Acquisti et al.   MOLECULAR BIOLOGY AND EVOLUTION

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Coding-Sequence Determinants of Gene Expression in Escherichia coli

(2009) G. Kudla et al.   SCIENCE

Origin of an Alternative Genetic Code in the Extremely Small and GC–Rich Genome of a Bacterial Symbiont

(2009) John P. McCutcheon et al.   PLoS Genetics

Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species

(2008) Oliver Keller et al.   BMC BIOINFORMATICS

HOST-RANGE EVOLUTION INAPHIDIUSPARASITOIDS: FIDELITY, VIRULENCE AND FITNESS TRADE-OFFS ON AN ANCESTRAL HOST

(2008) Lee M. Henry et al.   EVOLUTION

Brain Sex Differences and Function of thefruitlessGene inDrosophila

(2008) Daisuke Yamamoto   JOURNAL OF NEUROGENETICS

Wolbachia: master manipulators of invertebrate biology

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

Efficient and Accurate Construction of Genetic Linkage Maps from the Minimum Spanning Tree of a Graph

(2008) Yonghui Wu et al.   PLoS Genetics

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY

Sex Determination in the Hymenoptera

(2007) George E. Heimpel et al.   Annual Review of Entomology