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

[1]  Bartlomiej J. Troczka,et al.  Transposon-mediated insertional mutagenesis unmasks recessive insecticide resistance in the aphid Myzus persicae , 2021, Proceedings of the National Academy of Sciences.

[2]  D. Swarbreck,et al.  An aphid RNA transcript migrates systemically within plants and is a virulence factor , 2020, Proceedings of the National Academy of Sciences.

[3]  R. Nauen,et al.  The genetic architecture of a host shift: An adaptive walk protected an aphid and its endosymbiont from plant chemical defenses , 2020, Science Advances.

[4]  R. Nauen,et al.  Identification and functional characterization of a novel acetyl-CoA carboxylase mutation associated with ketoenol resistance in Bemisia tabaci. , 2020, Pesticide biochemistry and physiology.

[5]  D. Swarbreck,et al.  Chromosome-Scale Genome Assemblies of Aphids Reveal Extensively Rearranged Autosomes and Long-Term Conservation of the X Chromosome , 2020, bioRxiv.

[6]  Derek Warner,et al.  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, International journal of biological macromolecules.

[7]  Jennifer Lu,et al.  Improved metagenomic analysis with Kraken 2 , 2019, Genome Biology.

[8]  Steven L Salzberg,et al.  Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype , 2019, Nature Biotechnology.

[9]  Thomas E. Smith,et al.  Gene Family Evolution in the Pea Aphid Based on Chromosome-Level Genome Assembly , 2019, Molecular biology and evolution.

[10]  Yu Lin,et al.  Assembly of long, error-prone reads using repeat graphs , 2018, Nature Biotechnology.

[11]  C. Robin,et al.  What can genetic association panels tell us about evolutionary processes in insects? , 2019, Current opinion in insect science.

[12]  Heng Li,et al.  Fast and accurate long-read assembly with wtdbg2 , 2019, Nature Methods.

[13]  A. Borneman,et al.  Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies , 2018, BMC Bioinformatics.

[14]  Z. Fei,et al.  Genome sequence of the corn leaf aphid (Rhopalosiphum maidis Fitch) , 2019, GigaScience.

[15]  N. Hawkins,et al.  The evolutionary origins of pesticide resistance , 2018, Biological reviews of the Cambridge Philosophical Society.

[16]  Sanjit S. Batra,et al.  The Juicebox Assembly Tools module facilitates de novo assembly of mammalian genomes with chromosome-length scaffolds for under $1000 , 2018, bioRxiv.

[17]  R. Nauen,et al.  Neofunctionalization of Duplicated P450 Genes Drives the Evolution of Insecticide Resistance in the Brown Planthopper , 2018, Current Biology.

[18]  C. Lemaitre,et al.  Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches , 2017, Microbiome.

[19]  Alistair Miles,et al.  Genetic diversity of the African malaria vector Anopheles gambiae , 2017, Nature.

[20]  Michael S. Crossley,et al.  Landscape genomics of Colorado potato beetle provides evidence of polygenic adaptation to insecticides , 2017, Molecular ecology.

[21]  M. Williamson,et al.  Evolution of imidacloprid resistance in Myzus persicae in Greece and susceptibility data for spirotetramat. , 2017, Pest management science.

[22]  Mark Blaxter,et al.  BlobTools: Interrogation of genome assemblies , 2017, F1000Research.

[23]  P. Umina,et al.  Susceptibility of Australian Myzus persicae (Hemiptera: Aphididae) to Three Recently Registered Insecticides: Spirotetramat, Cyantraniliprole, and Sulfoxaflor , 2017, Journal of Economic Entomology.

[24]  S. Koren,et al.  Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation , 2016, bioRxiv.

[25]  Neva C. Durand,et al.  De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds , 2016, Science.

[26]  Niranjan Nagarajan,et al.  Fast and accurate de novo genome assembly from long uncorrected reads. , 2017, Genome research.

[27]  S. Endesfelder,et al.  Reduction of cortical parvalbumin expressing GABAergic interneurons in a rodent hyperoxia model of preterm birth brain injury with deficits in social behavior and cognition. , 2021, Development.

[28]  Bernardo J. Clavijo,et al.  Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species , 2017, Genome Biology.

[29]  Simon C. Groen,et al.  A genomic perspective on the generation and maintenance of genetic diversity in herbivorous insects. , 2016, Annual review of ecology, evolution, and systematics.

[30]  Yan Li,et al.  SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation , 2016, PloS one.

[31]  Daniel Mapleson,et al.  KAT: a K-mer analysis toolkit to quality control NGS datasets and genome assemblies , 2016, bioRxiv.

[32]  Neva C. Durand,et al.  Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. , 2016, Cell systems.

[33]  M. Schatz,et al.  Phased diploid genome assembly with single-molecule real-time sequencing , 2016, Nature Methods.

[34]  S. Salzberg,et al.  Centrifuge: rapid and sensitive classification of metagenomic sequences , 2016, bioRxiv.

[35]  James G. Baldwin-Brown,et al.  Contiguous and accurate de novo assembly of metazoan genomes with modest long read coverage , 2016, bioRxiv.

[36]  David S. Wishart,et al.  Heatmapper: web-enabled heat mapping for all , 2016, Nucleic Acids Res..

[37]  Daisy E. Pagete.  An end-to-end assembly of the Aedes aegypti genome , 2016, 1605.04619.

[38]  Katharina J. Hoff,et al.  BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS , 2015, Bioinform..

[39]  J. Peccoud,et al.  Genomics of adaptation to host-plants in herbivorous insects. , 2015, Briefings in functional genomics.

[40]  Evgeny M. Zdobnov,et al.  BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs , 2015, Bioinform..

[41]  K. Dang,et al.  Identification of putative kdr mutations in the tropical bed bug, Cimex hemipterus (Hemiptera: Cimicidae). , 2015, Pest management science.

[42]  Eunjung Han,et al.  Fast and accurate site frequency spectrum estimation from low coverage sequence data , 2015, Bioinform..

[43]  A. von Haeseler,et al.  IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies , 2014, Molecular biology and evolution.

[44]  Philipp W. Messer,et al.  Recent Selective Sweeps in North American Drosophila melanogaster Show Signatures of Soft Sweeps , 2013, PLoS genetics.

[45]  Christina A. Cuomo,et al.  Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement , 2014, PloS one.

[46]  M. Panini,et al.  Detecting the presence of target-site resistance to neonicotinoids and pyrethroids in Italian populations of Myzus persicae. , 2014, Pest management science.

[47]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[48]  S. Foster,et al.  The evolution of insecticide resistance in the peach potato aphid, Myzus persicae. , 1998, Insect biochemistry and molecular biology.

[49]  Zhijie Jiang,et al.  Comparative analysis of genome sequences from four strains of the Buchnera aphidicola Mp endosymbion of the green peach aphid, Myzus persicae , 2013, BMC Genomics.

[50]  R. Nauen,et al.  Gene amplification and microsatellite polymorphism underlie a recent insect host shift , 2013, Proceedings of the National Academy of Sciences.

[51]  Mauricio O. Carneiro,et al.  From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline , 2013, Current protocols in bioinformatics.

[52]  J. Simon,et al.  Dramatic Changes in the Genotypic Frequencies of Target Insecticide Resistance in French Populations of Myzus persicae (Hemiptera: Aphididae) Over the Last Decade , 2013, Journal of economic entomology.

[53]  R. ffrench-Constant,et al.  The Molecular Genetics of Insecticide Resistance , 2013, Genetics.

[54]  Heng Li.  Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM , 2013, 1303.3997.

[55]  F. Mahéo,et al.  The genetics of obligate parthenogenesis in an aphid species and its consequences for the maintenance of alternative reproductive modes , 2012, Heredity.

[56]  Kevin R. Thornton,et al.  The Drosophila melanogaster Genetic Reference Panel , 2012, Nature.

[57]  Youjun Zhang,et al.  Frequencies of the M918I mutation in the sodium channel of the diamondback moth in China, Thailand and Japan and its association with pyrethroid resistance , 2012 .

[58]  D. Falush,et al.  Inference of Population Structure using Dense Haplotype Data , 2012, PLoS genetics.

[59]  Heng Li,et al.  A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data , 2011, Bioinform..

[60]  Mark Borodovsky,et al.  Eukaryotic Gene Prediction Using GeneMark.hmm‐E and GeneMark‐ES , 2011, Current protocols in bioinformatics.

[61]  C. Brazier,et al.  Uncommon associations in target resistance among French populations of Myzus persicae from oilseed rape crops. , 2011, Pest management science.

[62]  Kenneth Lange,et al.  Enhancements to the ADMIXTURE algorithm for individual ancestry estimation , 2011, BMC Bioinformatics.

[63]  Gonçalo R. Abecasis,et al.  The variant call format and VCFtools , 2011, Bioinform..

[64]  Andrew J. Crossthwaite,et al.  Mutation of a nicotinic acetylcholine receptor β subunit is associated with resistance to neonicotinoid insecticides in the aphid Myzus persicae , 2011, BMC Neuroscience.

[65]  A. Wilson,et al.  The invasion route for an insect pest species: the tobacco aphid in the New World , 2010, Molecular ecology.

[66]  Martin J. Donnelly,et al.  Association Mapping of Insecticide Resistance in Wild Anopheles gambiae Populations: Major Variants Identified in a Low-Linkage Disequilbrium Genome , 2010, PloS one.

[67]  L. Excoffier,et al.  Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows , 2010, Molecular ecology resources.

[68]  G. K. Davis,et al.  Genome Sequence of the Pea Aphid Acyrthosiphon pisum , 2010, PLoS biology.

[69]  N. Moran,et al.  Facultative symbionts in aphids and the horizontal transfer of ecologically important traits. , 2010, Annual review of entomology.

[70]  I. Amit,et al.  Comprehensive mapping of long range interactions reveals folding principles of the human genome , 2011 .

[71]  M. Seagraves.  Aphids as Crop Pests , 2009 .

[72]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[73]  J. Peccoud,et al.  A continuum of genetic divergence from sympatric host races to species in the pea aphid complex , 2009, Proceedings of the National Academy of Sciences.

[74]  B. Fenton,et al.  Tracking the global dispersal of a cosmopolitan insect pest, the peach potato aphid , 2009, BMC Ecology.

[75]  C. Vorburger,et al.  Genetic variation and covariation of susceptibility to parasitoids in the aphid Myzus persicae: no evidence for trade-offs , 2008, Proceedings of the Royal Society B: Biological Sciences.

[76]  J. Pickup,et al.  Spatial and temporal dynamics of Myzus persicae clones in fields and suction traps , 2008 .

[77]  N. Moran.  Aphids as Crop Pests , 2008 .

[78]  S. Foster,et al.  Characterization of the M918T sodium channel gene mutation associated with strong resistance to pyrethroid insecticides in the peach-potato aphid, Myzus persicae (Sulzer) , 2007, Bulletin of Entomological Research.

[79]  Cecilia Tamborindeguy,et al.  Genomic resources for Myzus persicae: EST sequencing, SNP identification, and microarray design , 2007, BMC Genomics.

[80]  Anne-Béatrice Dufour,et al.  The ade4 Package: Implementing the Duality Diagram for Ecologists , 2007 .

[81]  Manuel A. R. Ferreira,et al.  PLINK: a tool set for whole-genome association and population-based linkage analyses. , 2007, American journal of human genetics.

[82]  R. Blackman,et al.  Microsatellite DNA and behavioural studies provide evidence of host-mediated speciation in Myzus persicae (Hemiptera: Aphididae) , 2007 .

[83]  R. Harrington,et al.  Aphids as crop pests , 2007 .

[84]  A. Clark,et al.  Thrice Out of Africa: Ancient and Recent Expansions of the Honey Bee, Apis mellifera , 2006, Science.

[85]  D. Huson,et al.  Application of phylogenetic networks in evolutionary studies. , 2006, Molecular biology and evolution.

[86]  Burkhard Morgenstern,et al.  AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints , 2005, Nucleic Acids Res..

[87]  Mark Daly,et al.  Haploview: analysis and visualization of LD and haplotype maps , 2005, Bioinform..

[88]  M. Williamson,et al.  Identification of mutations conferring insecticide‐insensitive AChE in the cotton‐melon aphid, Aphis gossypii Glover , 2004, Insect molecular biology.

[89]  T. Nabeshima,et al.  An amino acid substitution on the second acetylcholinesterase in the pirimicarb-resistant strains of the peach potato aphid, Myzus persicae. , 2003, Biochemical and biophysical research communications.

[90]  R. Blackman,et al.  Co-existence of different host-adapted forms of the Myzus persicae group (Hemiptera: Aphididae) in southern Italy , 2003, Bulletin of Entomological Research.

[91]  R. Blackman,et al.  Life cycle variation of Myzus persicae (Hemiptera: Aphididae) in Greece , 2002, Bulletin of Entomological Research.

[92]  K. Katoh,et al.  MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. , 2002, Nucleic acids research.

[93]  J. Mallet,et al.  Host races in plant-feeding insects and their importance in sympatric speciation. , 2002, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[94]  P. Usherwood,et al.  The molecular interactions of pyrethroid insecticides with insect and mammalian sodium channels. , 2001, Pest management science.

[95]  K. Crandall,et al.  TCS: a computer program to estimate gene genealogies , 2000, Molecular ecology.

[96]  B. Wiegmann,et al.  Genetic, biochemical, and behavioral uniformity among populations of Myzus nicotianae and Myzus persicae , 2000 .

[97]  B. Wiegmann,et al.  Genetic Variation in the Myzus persicae Complex (Homoptera: Aphididae): Evidence for a Single Species , 2000 .

[98]  A. Devonshire,et al.  A sodium channel point mutation is associated with resistance to DDT and pyrethroid insecticides in the peach‐potato aphid, Myzus persicae (Sulzer) (Hemiptera: Aphididae) , 1999, Insect molecular biology.

[99]  R. ffrench-Constant,et al.  Duplication of the Rdl GABA receptor subunit gene in an insecticide-resistant aphid, Myzus persicae , 1998, Molecular and General Genetics MGG.

[100]  A. Devonshire,et al.  Molecular studies of knockdown resistance to pyrethroids: cloning of domain II sodium channel gene sequences from insects , 1997 .

[101]  L. Excoffier,et al.  Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. , 1992, Genetics.

[102]  R. Blackman.  Morphological discrimination of a tobacco-feeding form from Myzus persicae (Sulzer) (Hemiptera: Aphididae), and a key to New World Myzus (Nectarosiphon) species , 1987 .

[103]  Nicholas H. Barton,et al.  The Relative Rates of Evolution of Sex Chromosomes and Autosomes , 1987, The American Naturalist.

[104]  J. A. Mckenzie,et al.  Ecological genetics of insecticide and acaricide resistance. , 1987, Annual review of entomology.

[105]  R. Blackman.  Chromosome numbers in the Aphididae and their taxonomic significance , 1980 .

[106]  S. U. Karaağaç.  INSECTICIDE resistance. , 1958, Canadian Medical Association journal.