title: Transcriptome profiling of a spirodiclofen susceptible and resistant strain of the European red mite Panonychus ulmi using strand-specific RNA-seq.
abstract: BACKGROUND
  The European red mite, Panonychus ulmi, is among the most important mite pests in fruit orchards, where it is controlled primarily by acaricide application. However, the species rapidly develops pesticide resistance, and the elucidation of resistance mechanisms for P. ulmi has not kept pace with insects or with the closely related spider mite Tetranychus urticae. The main reason for this lack of knowledge has been the absence of genomic resources needed to investigate the molecular biology of resistance mechanisms.
  
  
  RESULTS
  Here, we provide a comprehensive strand-specific RNA-seq based transcriptome resource for P. ulmi derived from strains susceptible and resistant to the widely used acaricide spirodiclofen. From a de novo assembly of the P. ulmi transcriptome, we manually annotated detoxification enzyme families, target-sites of commonly used acaricides, and horizontally transferred genes implicated in plant-mite interactions and pesticide resistance. In a comparative analysis that incorporated sequences available for Panonychus citri, T. urticae, and insects, we identified radiations for detoxification gene families following the divergence of Panonychus and Tetranychus genera. Finally, we used the replicated RNA-seq data from the spirodiclofen susceptible and resistant strains to describe gene expression changes associated with resistance. A cytochrome P450 monooxygenase, as well as multiple carboxylcholinesterases, were differentially expressed between the susceptible and resistant strains, and provide a molecular entry point for understanding resistance to spirodiclofen, widely used to control P. ulmi populations.
  
  
  CONCLUSIONS
  The new genomic resources and data that we present in this study for P. ulmi will substantially facilitate molecular studies of underlying mechanisms involved in acaricide resistance.
authors.affiliation: Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 9424, 1090, GE, Amsterdam, The Netherlands.
authors.forename: Sabina
authors.initials: S
authors.lastname: Bajda
authors.affiliation: Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium. wannes.dermauw@ugent.be.
authors.forename: Wannes
authors.initials: W
authors.lastname: Dermauw
authors.affiliation: Department of Biology, University of Utah, Salt Lake City, 257 South 1400 East, UT, 84112, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Greenhalgh
authors.affiliation: Bayer CropScience AG, Research Pest Control, Alfred Nobel Str. 50, D-40789, Monheim, Germany.
authors.forename: Ralf
authors.initials: R
authors.lastname: Nauen
authors.affiliation: Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium.
authors.forename: Luc
authors.initials: L
authors.lastname: Tirry
authors.affiliation: Department of Biology, University of Utah, Salt Lake City, 257 South 1400 East, UT, 84112, USA.|Center for Cell and Genome Science, University of Utah, Salt Lake City, 257 South 1400 East, UT, 84112, USA.
authors.forename: Richard M
authors.initials: RM
authors.lastname: Clark
authors.affiliation: Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 9424, 1090, GE, Amsterdam, The Netherlands. thomas.vanleeuwen@ugent.be.|Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000, Ghent, Belgium. thomas.vanleeuwen@ugent.be.
authors.forename: Thomas
authors.initials: T
authors.lastname: Van Leeuwen
mesh_terms: D015107:4-Butyrolactone / Q000031:analogs & derivatives* / Q000494:pharmacology; D056810:Acaricides / Q000494:pharmacology*; D000818:Animals; D004351:Drug Resistance / Q000235:genetics*; D020869:Gene Expression Profiling; D063990:Gene Ontology; D022761:Gene Transfer, Horizontal; D017423:Sequence Analysis, RNA; D013045:Species Specificity; D013141:Spiro Compounds / Q000494:pharmacology*; D040102:Tetranychidae / Q000187:drug effects* / Q000201:enzymology / Q000235:genetics*; D015262:Xenobiotics / Q000494:pharmacology
chemical_list: D056810:Acaricides; D013141:Spiro Compounds; D015262:Xenobiotics; C508135:spirodiclofen; D015107:4-Butyrolactone