Bajda et al. BMC Genomics (2015) 16:974 DOI 10.1186/s12864-015-2157-1 RESEARCH ARTICLE Open Access Transcriptome profiling of a spirodiclofen susceptible and resistant strain of the European red mite Panonychus ulmi using strand-specific RNA-seq Sabina Bajda1†, Wannes Dermauw2*† , Robert Greenhalgh3, Ralf Nauen4, Luc Tirry2, Richard M. Clark3,5 and Thomas Van Leeuwen1,2* 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. Keywords: Cyclic keto-enols, Tetranychidae, Target-site mutation, biRNA virus, Spirotetramat, Intradiol ring-cleavage dioxygenases, UDP-glycosyltransferases, Cytochrome P450 mono-oxygenases, Carboxyl/cholinesterases, Gluthathione-S-transferases * Correspondence: [email protected]; thomas.vanleeuwen@ugent. be †Equal contributors 2Laboratory of Agrozoology, Department of Crop Protection, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium 1Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, P.O. Box 94241090GE, Amsterdam, The Netherlands Full list of author information is available at the end of the article © 2015 Bajda et al. Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. Bajda et al. BMC Genomics (2015) 16:974 Page 2 of 26 Background for the detoxification enzymes associated with these ac- The European red mite, Panonychus ulmi, is a member tivities (CYP392E10 and TuCCE-04) [20]. It is clear that of the family Tetranychidae (Arthropoda: Chelicerata: our understanding of resistance to acaricides in phyt- Arachnida: Acari). Tetranychidae, or spider mites, use ophagous mites improved with the advent of the T. urti- their stylet- like chelicerae to puncture the leaf mesophyll- cae genome, however, such genomic resources are scarce cells to suck out cell contents. This results in chlorotic for other key tetranychid mites, particularly P. ulmi. spots and necrosis and ultimately, leaf abscission [1]. As a With only 49 nucleotide sequences available in the NCBI result, among mite pests, spider mites are economically public database (accessed May 2015), P. ulmi resistance important with 80 % of the acaricide market used for their research at the molecular level has hardly been possible. control [2]. Nonetheless, a major problem associated with For organisms without a sequenced genome, de novo spider mite control is the rapid development of acaricide transcriptome assemblies provide an important starting resistance. Factors accelerating resistance evolution in- point for genomic analyses, and recent advances in high- clude not only the frequent use of acaricides, but also high throughput transcript sequencing have greatly contributed fecundity rates, arrhenotokous reproduction (on haploid to our understanding of gene expression and structure males selection is highly effective) and a short life cycle [26–29]. This is especially true in agricultural pest man- [3]. As a result, the two-spotted spider mite (Tetranychus agement, where the majority of pest species do not have a urticae)andP. ulmi have developed resistance to nearly reference genome and where the elucidation of resistance all acaricide classes [4] and rank among the top 10 of most mechanisms of insecticides is vital [30–34]. resistant arthropod species based on the number of In this study we used the Illumina HiSeq2000 technol- unique active ingredients for which resistance has been ogy to generate deep paired-end, strand-specific RNA-seq reported [2]. reads for two strains of P. ulmi. The first strain (HS) is The acaricides spirodiclofen and spiromesifen belong, susceptible to most currently used acaricides, while the together with the insecticide spirotetramat, to the family second strain (PSR-TK) was field collected and shown to of spirocyclic tetronic acids (keto-enols) and interrupt be resistant to a number of acaricides, including hexythia- lipid biosynthesis by direct inhibition of acetyl coenzyme zox and clofentezine. The strain also showed decreased A carboxylase (ACCase) [5, 6]. Introduced relatively re- susceptibility to spirodiclofen, and was further selected in cently to the market [7], spirodiclofen has been shown the laboratory until high levels of spirodiclofen resistance to be an effective tool in resistance management of tetra- (Resistance ratio of 7000) were reached [17]. Paired-end nychid mites. It shows good to excellent residual control RNAseq reads were used to assemble a P. ulmi transcrip- [8, 9] and is effective against spider mites resistant to tome, and with the same assembly methodology we con- different acaricide classes [10–16]. Although high levels structed two P. citri transcriptomes based on previously of spirodiclofen resistance have not yet been reported in published RNA-seq data available as single end reads [33, field populations, artificial selection studies have shown 34]. We then performed a phylogenetic classification of that spider mites have the potential to develop resistance Panonychus gene families involved in detoxification, such to spirodiclofen comparatively rapid in the laboratory as cytochrome P450 monooxygenases (CYPs), carboxyl- [17, 18]. Selection for resistance was undertaken with T. cholinesterases (CCEs), glutathione-S-transferases (GSTs), urticae, P. ulmi and P. citri and resistance in all species UDP-glycosyl transferases (UGTs) and ABC transporters was synergized by piperonylbutoxide (PBO), suggesting (ABCs), and searched for horizontally transferred genes the involvement of cytochrome P450s [17–19]. Strikingly, that were previously uncovered in the genome sequence for all three tetranychid species spirodiclofen resistance of T. urticae [21, 35–39]. Moreover, a differential expres- was age dependent. The concentration of spirodiclofen sion analysis between the acaricide susceptible and resist- causing 50 % lethality (LC50) in the resistant strains was ant P. ulmi strain allowed us to identify genes encoding much lower in eggs then in mobile stages, a finding proteins that are candidates for involvement in acaricide Demaeght et al. [20] suggested could be due to lower ex- resistance. In addition, we identified and compared P. pression of detoxification genes in eggs. ulmi expressed sequences for known acaricide target sites. In 2011, the high quality genome sequence of the The assembled annotated transcriptome of P. ulmi pro- spider mite Tetranychus urticae became available [21], vides an important resource that should substantially fa- and afforded new resources and tools to investigate the cilitate molecular studies in this species, including the molecular mechanisms underlying acaricide resistance elucidation of detoxification mechanisms of xenobiotics. [20, 22–25]. For example, although biochemical studies had shown that elevated P450 and esterase levels were Results and discussion associated with resistance to spirodiclofen in T. urticae De novo sequence assembly (see above), studies with a genome-wide gene expression We performed high-throughput Illumina sequencing microarray allowed the identification of the genes coding of RNA extracted from adult females from acaricide Bajda et al. BMC Genomics (2015) 16:974 Page 3 of 26 susceptible (HS) and resistant P. ulmi strains (PSR- model arthropod species (e.g. in