Transcriptome profiling of a spirodiclofen susceptible and resistant strain of the European red mite Panonychus ulmi using strand-specific RNA-seq
- Author
- Sabina Bajda, Wannes Dermauw (UGent) , Robert Greenhalgh, Ralf Nauen, Luc Tirry (UGent) , Richard M Clark and Thomas Van Leeuwen (UGent)
- Organization
- 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
- ABAMECTIN RESISTANCE, EXPRESSION ANALYSIS, UDP-GLYCOSYLTRANSFERASE, VIRUS-DISEASE, TRIALEURODES-VAPORARIORUM, INSECTICIDE-RESISTANCE, CROSS-RESISTANCE, CYTOCHROME-P450 GENES, 2-SPOTTED SPIDER-MITE, TETRANYCHUS-URTICAE ACARI, UDP-glycosyltransferases, Carboxyl/cholinesterases, Cyclic keto-enols, Gluthathione-S-transferases, biRNA virus, Cytochrome P450 mono-oxygenases, Spirotetramat, Target-site mutation, Tetranychidae, Intradiol ring-cleavage dioxygenases
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Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-7040148
- MLA
- Bajda, Sabina, et al. “Transcriptome Profiling of a Spirodiclofen Susceptible and Resistant Strain of the European Red Mite Panonychus Ulmi Using Strand-Specific RNA-Seq.” BMC GENOMICS, vol. 16, 2015, doi:10.1186/s12864-015-2157-1.
- APA
- Bajda, S., Dermauw, W., Greenhalgh, R., Nauen, R., Tirry, L., Clark, R. M., & Van Leeuwen, T. (2015). Transcriptome profiling of a spirodiclofen susceptible and resistant strain of the European red mite Panonychus ulmi using strand-specific RNA-seq. BMC GENOMICS, 16. https://doi.org/10.1186/s12864-015-2157-1
- Chicago author-date
- Bajda, Sabina, Wannes Dermauw, Robert Greenhalgh, Ralf Nauen, Luc Tirry, Richard M Clark, and Thomas Van Leeuwen. 2015. “Transcriptome Profiling of a Spirodiclofen Susceptible and Resistant Strain of the European Red Mite Panonychus Ulmi Using Strand-Specific RNA-Seq.” BMC GENOMICS 16. https://doi.org/10.1186/s12864-015-2157-1.
- Chicago author-date (all authors)
- Bajda, Sabina, Wannes Dermauw, Robert Greenhalgh, Ralf Nauen, Luc Tirry, Richard M Clark, and Thomas Van Leeuwen. 2015. “Transcriptome Profiling of a Spirodiclofen Susceptible and Resistant Strain of the European Red Mite Panonychus Ulmi Using Strand-Specific RNA-Seq.” BMC GENOMICS 16. doi:10.1186/s12864-015-2157-1.
- Vancouver
- 1.Bajda S, Dermauw W, Greenhalgh R, Nauen R, Tirry L, Clark RM, et al. Transcriptome profiling of a spirodiclofen susceptible and resistant strain of the European red mite Panonychus ulmi using strand-specific RNA-seq. BMC GENOMICS. 2015;16.
- IEEE
- [1]S. Bajda et al., “Transcriptome profiling of a spirodiclofen susceptible and resistant strain of the European red mite Panonychus ulmi using strand-specific RNA-seq,” BMC GENOMICS, vol. 16, 2015.
@article{7040148, 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.}}, articleno = {{974}}, author = {{Bajda, Sabina and Dermauw, Wannes and Greenhalgh, Robert and Nauen, Ralf and Tirry, Luc and Clark, Richard M and Van Leeuwen, Thomas}}, issn = {{1471-2164}}, journal = {{BMC GENOMICS}}, keywords = {{ABAMECTIN RESISTANCE,EXPRESSION ANALYSIS,UDP-GLYCOSYLTRANSFERASE,VIRUS-DISEASE,TRIALEURODES-VAPORARIORUM,INSECTICIDE-RESISTANCE,CROSS-RESISTANCE,CYTOCHROME-P450 GENES,2-SPOTTED SPIDER-MITE,TETRANYCHUS-URTICAE ACARI,UDP-glycosyltransferases,Carboxyl/cholinesterases,Cyclic keto-enols,Gluthathione-S-transferases,biRNA virus,Cytochrome P450 mono-oxygenases,Spirotetramat,Target-site mutation,Tetranychidae,Intradiol ring-cleavage dioxygenases}}, language = {{eng}}, pages = {{26}}, title = {{Transcriptome profiling of a spirodiclofen susceptible and resistant strain of the European red mite Panonychus ulmi using strand-specific RNA-seq}}, url = {{http://doi.org/10.1186/s12864-015-2157-1}}, volume = {{16}}, year = {{2015}}, }
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