A nuclear receptor HR96-related gene underlies large trans-driven differences in detoxification gene expression in a generalist herbivore

[1]  T. Van Leeuwen,et al.  A review of the molecular mechanisms of acaricide resistance in mites and ticks. , 2023, Insect biochemistry and molecular biology.

[2]  T. Van Leeuwen,et al.  Incomplete reproductive barriers and genomic differentiation impact the spread of resistance mutations between green‐ and red‐colour morphs of a cosmopolitan mite pest , 2023, Molecular ecology.

[3]  Silvio C. E. Tosatto,et al.  InterPro in 2022 , 2022, Nucleic Acids Res..

[4]  Richard M. Clark,et al.  Trans-driven variation in expression is common among detoxification genes in the extreme generalist herbivore Tetranychus urticae , 2022, PLoS genetics.

[5]  B. Vanholme,et al.  Intradiol ring cleavage dioxygenases from herbivorous spider mites as a new detoxification enzyme family in animals , 2022, BMC biology.

[6]  Steven J. Marygold,et al.  FlyBase: a guided tour of highlighted features , 2022, Genetics.

[7]  Paul Theodor Pyl,et al.  Analysing high-throughput sequencing data in Python with HTSeq 2.0 , 2021, Bioinform..

[8]  R. Nauen,et al.  The Role of Cytochrome P450s in Insect Toxicology and Resistance. , 2021, Annual review of entomology.

[9]  S. Ovchinnikov,et al.  ColabFold: making protein folding accessible to all , 2022, Nature Methods.

[10]  Oriol Vinyals,et al.  Highly accurate protein structure prediction with AlphaFold , 2021, Nature.

[11]  Richard M. Clark,et al.  Adaptive divergence and post-zygotic barriers to gene flow between sympatric populations of a herbivorous mite , 2021, Communications biology.

[12]  R. Nauen,et al.  Transcriptional regulation of xenobiotic detoxification genes in insects - An overview. , 2021, Pesticide biochemistry and physiology.

[13]  C. Bass,et al.  Changes in both trans- and cis-regulatory elements mediate insecticide resistance in a lepidopteron pest, Spodoptera exigua , 2021, PLoS genetics.

[14]  Richard M. Clark,et al.  High-resolution genetic mapping reveals cis-regulatory and copy number variation in loci associated with cytochrome P450-mediated detoxification in a generalist arthropod pest , 2021, bioRxiv.

[15]  T. Van Leeuwen,et al.  Short term transcriptional responses of P450s to phytochemicals in insects and mites , 2020, Current opinion in insect science.

[16]  P. Wittkopp,et al.  Molecular and evolutionary processes generating variation in gene expression , 2020, Nature Reviews Genetics.

[17]  Silvio C. E. Tosatto,et al.  The InterPro protein families and domains database: 20 years on , 2020, Nucleic Acids Res..

[18]  J. Khan.  STRUCTURE OF HUMAN PREGNANE X RECEPTOR LIGAND BINDING DOMAIN BOUND TETHERED WITH SRC co-activator peptide IN COMPLEX WITH (S,S)-1 , 2020 .

[19]  J. Vontas,et al.  Cytochrome P450-based metabolic insecticide resistance in Anopheles and Aedes mosquito vectors: Muddying the waters. , 2020, Pesticide biochemistry and physiology.

[20]  Ralf Nauen,et al.  Insecticides, biologics and nematicides: Updates to IRAC's mode of action classification - a tool for resistance management. , 2020, Pesticide biochemistry and physiology.

[21]  M. Riga,et al.  Targeted mutagenesis using CRISPR-Cas9 in the chelicerate herbivore Tetranychus urticae. , 2020, Insect biochemistry and molecular biology.

[22]  M. Riga,et al.  Targeted mutagenesis using CRISPR-Cas9 in the chelicerate herbivore Tetranychus urticae , 2019, bioRxiv.

[23]  R. Irizarry.  ggplot2 , 2019, Introduction to Data Science.

[24]  J. Hearn,et al.  Cis-regulatory CYP6P9b P450 variants associated with loss of insecticide-treated bed net efficacy against Anopheles funestus , 2019, Nature Communications.

[25]  Patrick Schweizer,et al.  siRNA-Finder (si-Fi) Software for RNAi-Target Design and Off-Target Prediction , 2019, Front. Plant Sci..

[26]  Richard M. Clark,et al.  High-resolution QTL mapping in Tetranychus urticae reveals acaricide-specific responses and common target-site resistance after selection by different METI-I acaricides. , 2019, Insect biochemistry and molecular biology.

[27]  D. Moras,et al.  A revisited version of the apo structure of the ligand-binding domain of the human nuclear receptor RXR-ALPHA , 2019 .

[28]  Richard M. Clark,et al.  Long-Term Population Studies Uncover the Genome Structure and Genetic Basis of Xenobiotic and Host Plant Adaptation in the Herbivore Tetranychus urticae , 2018, Genetics.

[29]  S. Kasai,et al.  CYP-mediated permethrin resistance in Aedes aegypti and evidence for trans-regulation , 2018, PLoS neglected tropical diseases.

[30]  T. Van Leeuwen,et al.  Transcriptomic Plasticity in the Arthropod Generalist Tetranychus urticae Upon Long-Term Acclimation to Different Host Plants , 2018, G3: Genes, Genomes, Genetics.

[31]  S. Morin,et al.  Species‐complex diversification and host‐plant associations in Bemisia tabaci: A plant‐defence, detoxification perspective revealed by RNA‐Seq analyses , 2018, Molecular ecology.

[32]  M Mirdita,et al.  MMseqs2 desktop and local web server app for fast, interactive sequence searches , 2018, bioRxiv.

[33]  Z. Brown,et al.  Wicked evolution: Can we address the sociobiological dilemma of pesticide resistance? , 2018, Science.

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

[35]  R. Feyereisen,et al.  Does host plant adaptation lead to pesticide resistance in generalist herbivores? , 2018, Current opinion in insect science.

[36]  Richard M. Clark,et al.  Disruption of a horizontally transferred phytoene desaturase abolishes carotenoid accumulation and diapause in Tetranychus urticae , 2017, Proceedings of the National Academy of Sciences.

[37]  Richard M. Clark,et al.  Complex Evolutionary Dynamics of Massively Expanded Chemosensory Receptor Families in an Extreme Generalist Chelicerate Herbivore , 2016, Genome biology and evolution.

[38]  Roland Eils,et al.  Complex heatmaps reveal patterns and correlations in multidimensional genomic data , 2016, Bioinform..

[39]  D. Chitwood,et al.  eQTL Regulating Transcript Levels Associated with Diverse Biological Processes in Tomato1[OPEN] , 2016, Plant Physiology.

[40]  T. Van Leeuwen,et al.  The Molecular Evolution of Xenobiotic Metabolism and Resistance in Chelicerate Mites. , 2016, Annual review of entomology.

[41]  M. Riga,et al.  Functional characterization of the Tetranychus urticae CYP392A11, a cytochrome P450 that hydroxylates the METI acaricides cyenopyrafen and fenpyroximate. , 2015, Insect biochemistry and molecular biology.

[42]  Kin-Fan Au,et al.  PacBio Sequencing and Its Applications , 2015, Genom. Proteom. Bioinform..

[43]  F. Hendrickx,et al.  Adaptation of a polyphagous herbivore to a novel host plant extensively shapes the transcriptome of herbivore and host , 2015, Molecular ecology.

[44]  Manuel Martínez,et al.  Digestive proteases in bodies and faeces of the two-spotted spider mite, Tetranychus urticae. , 2015, Journal of insect physiology.

[45]  R. Feyereisen,et al.  Genotype to phenotype, the molecular and physiological dimensions of resistance in arthropods. , 2015, Pesticide biochemistry and physiology.

[46]  R. Zeng,et al.  Insect response to plant defensive protease inhibitors. , 2015, Annual review of entomology.

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

[48]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[49]  D. Heckel,et al.  Bacterial origin of a diverse family of UDP-glycosyltransferase genes in the Tetranychus urticae genome. , 2014, Insect biochemistry and molecular biology.

[50]  M. Riga,et al.  Abamectin is metabolized by CYP392A16, a cytochrome P450 associated with high levels of acaricide resistance in Tetranychus urticae. , 2014, Insect biochemistry and molecular biology.

[51]  J. Oakeshott,et al.  How many genetic options for evolving insecticide resistance in heliothine and spodopteran pests? , 2013, Pest management science.

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

[53]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[54]  David W. Cheung,et al.  SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler , 2012, GigaScience.

[55]  Richard M. Clark,et al.  A link between host plant adaptation and pesticide resistance in the polyphagous spider mite Tetranychus urticae , 2012, Proceedings of the National Academy of Sciences.

[56]  Yves Van de Peer,et al.  ORCAE: online resource for community annotation of eukaryotes , 2012, Nature Methods.

[57]  B. Faircloth,et al.  Primer3—new capabilities and interfaces , 2012, Nucleic acids research.

[58]  Guangchuang Yu,et al.  clusterProfiler: an R package for comparing biological themes among gene clusters. , 2012, Omics : a journal of integrative biology.

[59]  Richard M. Clark,et al.  Population bulk segregant mapping uncovers resistance mutations and the mode of action of a chitin synthesis inhibitor in arthropods , 2012, Proceedings of the National Academy of Sciences.

[60]  Stefan R. Henz,et al.  The genome of Tetranychus urticae reveals herbivorous pest adaptations , 2011, Nature.

[61]  Y. Saeys,et al.  GenomeView: a next-generation genome browser , 2011, Nucleic acids research.

[62]  Andrey A. Shabalin,et al.  Matrix eQTL: ultra fast eQTL analysis via large matrix operations , 2011, Bioinform..

[63]  Hanbo Chen,et al.  VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R , 2011, BMC Bioinformatics.

[64]  M. DePristo,et al.  The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. , 2010, Genome research.

[65]  M. Goddard,et al.  Copy Number Variation and Transposable Elements Feature in Recent, Ongoing Adaptation at the Cyp6g1 Locus , 2010, PLoS genetics.

[66]  E. Hafen,et al.  The Nuclear Receptor DHR3 Modulates dS6 Kinase–Dependent Growth in Drosophila , 2010, PLoS genetics.

[67]  Ning Ma,et al.  BLAST+: architecture and applications , 2009, BMC Bioinformatics.

[68]  Hadley Wickham,et al.  ggplot2 - Elegant Graphics for Data Analysis (2nd Edition) , 2017 .

[69]  S. Kliewer,et al.  Nuclear receptor DAF-12 from parasitic nematode Strongyloides stercoralis in complex with its physiological ligand dafachronic acid delta 7 , 2009 .

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

[71]  David L Stern,et al.  The Loci of Evolution: How Predictable is Genetic Evolution? , 2008, Evolution; international journal of organic evolution.

[72]  G. Howe,et al.  Plant Interactions with Arthropod Herbivores: State of the Field , 2008, Plant Physiology.

[73]  C. Thummel,et al.  The DHR96 nuclear receptor regulates xenobiotic responses in Drosophila. , 2006, Cell metabolism.

[74]  M. Redinbo,et al.  Structure and function of the human nuclear xenobiotic receptor PXR. , 2005, Current drug metabolism.

[75]  H. Krause,et al.  The Drosophila Nuclear Receptor E75 Contains Heme and Is Gas Responsive , 2005, Cell.

[76]  C. Thummel,et al.  Nuclear receptors — a perspective from Drosophila , 2005, Nature Reviews Genetics.

[77]  L. Moore,et al.  crystal structure of CAR/RXR heterodimer bound with SRC1 peptide, fatty acid, and 5b-pregnane-3,20-dione. , 2004 .

[78]  Hao Wu,et al.  R/qtl: QTL Mapping in Experimental Crosses , 2003, Bioinform..

[79]  Blake C. Meyers,et al.  Genome-Wide Analysis of NBS-LRR–Encoding Genes in Arabidopsis Online version contains Web-only data. Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.009308. , 2003, The Plant Cell Online.

[80]  R. ffrench-Constant,et al.  A Single P450 Allele Associated with Insecticide Resistance in Drosophila , 2002, Science.

[81]  J. Sambrook,et al.  Molecular Cloning: A Laboratory Manual , 2001 .

[82]  D. Moras,et al.  CRYSTAL STRUCTURE OF THE NUCLEAR RECEPTOR FOR VITAMIN D COMPLEXED TO VITAMIN D , 2000 .

[83]  J. G. Scott,et al.  Cytochromes P450 and insecticide resistance. , 1999, Insect biochemistry and molecular biology.

[84]  R. Feyereisen,et al.  Constitutive overexpression of the cytochrome P450 gene CYP6A1 in a house fly strain with metabolic resistance to insecticides. , 1994, Insect biochemistry and molecular biology.

[85]  B. Hammock,et al.  Genetic and molecular evidence for a trans-acting regulatory locus controlling glutathione S-transferase-2 expression in Aedes aegypti , 1992, Molecular and General Genetics MGG.

[86]  L. Tirry,et al.  A mutation in the PSST homologue of complex I (NADH:ubiquinone oxidoreductase) from Tetranychus urticae is associated with resistance to METI acaricides. , 2017, Insect biochemistry and molecular biology.

[87]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[88]  Nick V Grishin,et al.  PROMALS3D: multiple protein sequence alignment enhanced with evolutionary and three-dimensional structural information. , 2014, Methods in molecular biology.

[89]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[90]  R. Feyereisen.  Insect CYP Genes and P450 Enzymes , 2012 .

[91]  Cedric E. Ginestet.  ggplot2: Elegant Graphics for Data Analysis , 2011 .

[92]  May R Berenbaum,et al.  Molecular mechanisms of metabolic resistance to synthetic and natural xenobiotics. , 2007, Annual review of entomology.

[93]  R. Michelmore,et al.  Genome-Wide Analysis of NBS-LRR–Encoding Genes in Arabidopsis Online version contains Web-only data. Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.009308. , 2003, The Plant Cell Online.