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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.    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-2157-1) contains supplementary material, which is available to authorized users.

Transcriptome profiling of a spirodiclofen susceptible and resistant strain of the European red mite Panonychus ulmi using strand-specific RNA-seq