Abundant trans-driven variation in detoxification gene expression in the extreme generalist herbivore Tetranychus urticae

Abstract

The extreme adaptation potential of the generalist herbivore Tetranychus urticae (the two-spotted spider mite) to pesticides as well as diverse host plants has been associated with clade-specific gene expansions in known detoxifying enzyme families, and with extensive and rapid transcriptional responses. However, how this broad transcriptional potential is regulated remains largely unknown. Using a parental/F1 design in which four inbred strains were crossed to a common inbred strain, we assessed the genetic basis and inheritance of gene expression variation in T. urticae. Mirroring known phenotypic variation in the progenitor strains of the inbreds, we confirmed that the inbred strains we created were genetically distinct, varied markedly in pesticide resistance, and also captured variation in host plant fitness commonly observed in this species. By examining differences in gene expression between parents and allele-specific expression in F1s, we found that variation in RNA abundance was more often explained in trans as compared to cis, with the former associated with dominance in inheritance. Strikingly, in a gene ontology analysis, detoxification genes of the cytochrome P450 monooxygenase (CYP) family, as well as dioxygenases (DOGs) acquired from horizontal gene transfer from fungi, were specifically enriched at the extremes of trans-driven up- and downregulation. In particular, a clade of CYPs with documented broad substrate-specificity including multiple pesticides, as well as DOGs that have recently been shown to have broad substrate specificity against plant specialized compounds, were exceptionally highly upregulated as a result of trans effects (or in some cases synergism of cis and trans) in the most multi-pesticide resistant strains. Collectively, our findings highlight the potential importance of trans-driven expression variation in genes associated with xenobiotic metabolism and host plant use for rapid adaptation in T. urticae, and also suggest modular control of these genes, a regulatory architecture that might ameliorate negative pleiotropic effects.

High-Resolution Genetic Mapping Combined with Transcriptome Profiling Reveals That Both Target-Site Resistance and Increased Detoxification Confer Resistance to the Pyrethroid Bifenthrin in the Spider Mite Tetranychus urticae

“…Further, the presence of an L925M mutation in the VGSC of the highly bifenthrin-resistant strain ROS-IT and its loss in its susceptible derivative inbred line indicated the importance of the L925M mutation in bifenthrin resistance. Very recently, this mutation was also reported for bifenthrin-resistant T. urticae strains in a study investigating gene regulation mechanisms [ 20 ]. Notably, amino acid substitutions at this VGSC position—leucine to valine (L925V), methionine (L925M) or isoleucine (L925I)—have also been correlated with pyrethroid resistance in other mites and ticks, including the Varroa mite, the poultry red mite D. gallinae , predatory mites such as P. persimilis [ 26 , 27 , 29 , 80 ], the cattle tick Rhipicephalus microplus and insects such as the common bedbug Cimex lectularius and several species of whiteflies [ 10 ].…”

“…This might suggest that the expression of these genes is regulated by a trans acting factor. Recently, such trans -driven regulation of detoxification genes has been clearly demonstrated for T. urticae [ 20 ], and therefore, we also examined QTL1 for transcription factors. In the QTL1 region [ 20 ], we found an E75 nuclear receptor which was significantly upregulated (log 2 FC of 3.51) in the differential gene expression analysis comparing all resistant to all susceptible strains.…”

“…This study also uses inbred (suffix i) strains (MR-VLi, SR6i and ROS-ITi) derived from subpopulations of the MR-VL, SR6 and ROS-IT cultures, which were made inbred by seven to eight generations of consecutive mother–son mating, as described by Bryon et al [ 55 ]. All inbred strains used in this study were described earlier in Kurlovs et al [ 20 ] and in De Beer et al [ 52 ].…”

“…Based on the gene expression data and DNA sequences available from this study (see Section 2.5 and Section 2.6 for sequencing and mapping details) and previous studies [ 52 , 54 ], all T. urticae strains used in this study were screened for the presence of VGSC mutations (M918L, L925M, L1024V, F1534S, F1538I; M. domestica numbering) previously shown to be associated with pyrethroid resistance in T. urticae [ 16 , 19 , 20 ]. Briefly, since the number of RNAseq read counts aligning with the VGSC gene was low for the strains El Juan, MR-VL, ES1, IT3, ROS-IT, UK4 and RO1, the presence of the aforementioned mutations was visually examined using the Integrative Genomics Viewer [ 57 ], and the mutation was considered present when the mutation was observed in at least 20% of the reads.…”

“…In follow-up studies, the reduced insecticide binding was attributed to the presence of mutations in the VGSC, with the kdr mutation (L1014F) being documented globally in many major arthropod pests and disease vectors (reviewed in Rinkevich, Du and Dong [ 10 ]). For the Tetranychus species, several mutations in the VGSC have also been associated with decreased sensitivity towards Type I and Type II pyrethroids: point mutations M918L/T or L925M in the intracellular linker connecting transmembrane segments IIS4 and IIS5 (where M918L was found in combination with F1534S in IIIS6), L1024V at the terminus of the IIS6 transmembrane segment of the sodium channel and F1538I in domain IIIS6 ( M. domestica numbering) [ 16 , 17 , 18 , 19 , 20 , 21 ] ( Figure 1 ) ( Table S1 ). Similar VGSC mutations have also been reported for other spider mites such as Panonychus citri and Panonychus ulmi , but also in other mites and ticks, including the cattle tick Rhipicephalus microplus , the Varroa mite, the poultry red mite Dermanyssus gallinae and predatory mites such as Phytoseiulus persimilis [ 22 , 25 , 26 , 27 , 28 , 29 , 30 , 31 ].…”