Global patterns in genomic diversity underpinning the evolution of insecticide resistance in the aphid crop pest Myzus persicae

Transposon-mediated insertional mutagenesis unmasks recessive insecticide resistance in the aphid Myzus persicae

(2021) Michela Panini et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characteristic and variability of five complete aphid mitochondrial genomes: Aphis fabae mordvilkoi, Aphis craccivora, Myzus persicae, Therioaphis tenera and Appendiseta robiniae (Hemiptera; Sternorrhyncha; Aphididae)

(2020) Nina V. Voronova et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

An aphid RNA transcript migrates systemically within plants and is a virulence factor

(2020) Yazhou Chen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genetic architecture of a host shift: An adaptive walk protected an aphid and its endosymbiont from plant chemical defenses

(2020) Kumar Saurabh Singh et al.   Science Advances

Identification and functional characterization of a novel acetyl-CoA carboxylase mutation associated with ketoenol resistance in Bemisia tabaci

(2020) Bettina Lueke et al.   PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY

Chromosome-scale genome assemblies of aphids reveal extensively rearranged autosomes and long-term conservation of the X chromosome

(2020) Thomas C Mathers et al.   MOLECULAR BIOLOGY AND EVOLUTION

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

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

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

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Fast and accurate long-read assembly with wtdbg2

(2019) Jue Ruan et al.   NATURE METHODS

The evolutionary origins of pesticide resistance

(2018) Nichola J. Hawkins et al.   BIOLOGICAL REVIEWS

Neofunctionalization of Duplicated P450 Genes Drives the Evolution of Insecticide Resistance in the Brown Planthopper

(2018) Christoph T. Zimmer et al.   CURRENT BIOLOGY

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies

(2018) Michael J. Roach et al.   BMC BIOINFORMATICS

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

(2018) Cervin Guyomar et al.   Microbiome

What can genetic association panels tell us about evolutionary processes in insects?

(2018) Charles Robin et al.   Current Opinion in Insect Science

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

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

(2017) Sergey Koren et al.   GENOME RESEARCH

Susceptibility of Australian Myzus persicae (Hemiptera: Aphididae) to Three Recently Registered Insecticides: Spirotetramat, Cyantraniliprole, and Sulfoxaflor

(2017) Siobhan C. de Little et al.   JOURNAL OF ECONOMIC ENTOMOLOGY

Landscape genomics of Colorado potato beetle provides evidence of polygenic adaptation to insecticides

(2017) Michael S. Crossley et al.   MOLECULAR ECOLOGY

Genetic diversity of the African malaria vector Anopheles gambiae

(2017) Alistair Miles et al.   NATURE

Evolution of imidacloprid resistance in Myzus persicae in Greece and susceptibility data for spirotetramat

(2017) Costas Ch Voudouris et al.   PEST MANAGEMENT SCIENCE

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

A Genomic Perspective on the Generation and Maintenance of Genetic Diversity in Herbivorous Insects

(2016) Andrew D. Gloss et al.   Annual Review of Ecology Evolution and Systematics

Centrifuge: rapid and sensitive classification of metagenomic sequences

(2016) Daehwan Kim et al.   GENOME RESEARCH

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

Heatmapper: web-enabled heat mapping for all

(2016) Sasha Babicki et al.   NUCLEIC ACIDS RESEARCH

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

(2016) Wei Shen et al.   PLoS One

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS: Table 1.

(2015) Katharina J. Hoff et al.   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Genomics of adaptation to host-plants in herbivorous insects

(2015) J.-C. Simon et al.   Briefings in Functional Genomics

Recent Selective Sweeps in North American Drosophila melanogaster Show Signatures of Soft Sweeps

(2015) Nandita R. Garud et al.   PLoS Genetics

Fast and accurate site frequency spectrum estimation from low coverage sequence data

(2014) Eunjung Han et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The evolution of insecticide resistance in the peach potato aphid, Myzus persicae

(2014) Chris Bass et al.   INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Identification of putativekdrmutations in the tropical bed bug,Cimex hemipterus(Hemiptera: Cimicidae)

(2014) Kai Dang et al.   PEST MANAGEMENT SCIENCE

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

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

Comparative analysis of genome sequences from four strains of the Buchnera aphidicola Mp endosymbion of the green peach aphid, Myzus persicae

(2013) Zhijie Jiang et al.   BMC GENOMICS

The Molecular Genetics of Insecticide Resistance

(2013) Richard H. ffrench-Constant   GENETICS

Dramatic Changes in the Genotypic Frequencies of Target Insecticide Resistance in French Populations of Myzus persicae (Hemiptera: Aphididae) Over the Last Decade

(2013) Lise Roy et al.   JOURNAL OF ECONOMIC ENTOMOLOGY

Detecting the presence of target-site resistance to neonicotinoids and pyrethroids in Italian populations ofMyzus persicae

(2013) Michela Panini et al.   PEST MANAGEMENT SCIENCE

Gene amplification and microsatellite polymorphism underlie a recent insect host shift

(2013) C. Bass et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genetics of obligate parthenogenesis in an aphid species and its consequences for the maintenance of alternative reproductive modes

(2012) C-A Dedryver et al.   HEREDITY

The Drosophila melanogaster Genetic Reference Panel

(2012) Trudy F. C. Mackay et al.   NATURE

Inference of Population Structure using Dense Haplotype Data

(2012) Daniel John Lawson et al.   PLoS Genetics

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

Enhancements to the ADMIXTURE algorithm for individual ancestry estimation

(2011) David H Alexander et al.   BMC BIOINFORMATICS

Mutation of a nicotinic acetylcholine receptor β subunit is associated with resistance to neonicotinoid insecticides in the aphid Myzus persicae

(2011) Chris Bass et al.   BMC NEUROSCIENCE

Uncommon associations in target resistance among French populations of Myzus persicae from oilseed rape crops

(2011) Séverine Fontaine et al.   PEST MANAGEMENT SCIENCE

Frequencies of the M918I mutation in the sodium channel of the diamondback moth in China, Thailand and Japan and its association with pyrethroid resistance

(2011) Shoji Sonoda et al.   PESTICIDE BIOCHEMISTRY AND PHYSIOLOGY

The invasion route for an insect pest species: the tobacco aphid in the New World

(2010) F. A. ZEPEDA-PAULO et al.   MOLECULAR ECOLOGY

Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows

(2010) LAURENT EXCOFFIER et al.   Molecular Ecology Resources

Association Mapping of Insecticide Resistance in Wild Anopheles gambiae Populations: Major Variants Identified in a Low-Linkage Disequilbrium Genome

(2010) David Weetman et al.   PLoS One

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

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

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Tracking the global dispersal of a cosmopolitan insect pest, the peach potato aphid

(2009) John T Margaritopoulos et al.   BMC ECOLOGY

Spatial and temporal dynamics of Myzus persicae clones in fields and suction traps

(2008) Louise Kasprowicz et al.   AGRICULTURAL AND FOREST ENTOMOLOGY