Trans-driven variation in expression is common among detoxification genes 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 as is 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, multiple CYPs and DOGs with broad substrate-specificities for pesticides or plant specialized compounds were exceptionally highly upregulated as a result of trans-regulatory variation, 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 suggests modular control of these genes, a regulatory architecture that might ameliorate negative pleiotropic effects.

Intraspecific diversity in the mechanisms underlying abamectin resistance in a cosmopolitan pest

“…A differential gene expression analysis between pairs of abamectin-resistant and susceptible parental lines, i.e. MAR-ABi versus SOL-BEi and ROS-ITi versus JP-RRi, was performed using previously available data described in Kurlovs et al, (2022). Briefly, in Kurlovs et al, 2022, total RNA was extracted from a pool of 100–120 adult females per line using the RNeasy plus mini kit (Qiagen, Belgium) with 4 replicates for strains MAR-ABi and JP-RRi and 5 replicates for strains ROS-ITi and SOL-BEi.…”

“…MAR-ABi versus SOL-BEi and ROS-ITi versus JP-RRi, was performed using previously available data described in Kurlovs et al, (2022). Briefly, in Kurlovs et al, 2022, total RNA was extracted from a pool of 100–120 adult females per line using the RNeasy plus mini kit (Qiagen, Belgium) with 4 replicates for strains MAR-ABi and JP-RRi and 5 replicates for strains ROS-ITi and SOL-BEi. The concentration and purity of the RNA samples were assessed using a DeNovix DS-11 spectrophotometer (DeNovix, Willmington, DE, USA) and checked visually via gel electrophoresis (1% agarose gel; 30 min; 100V).…”

“…For the other parental strains, SOL-BEi, MAR-ABi and JP-RRi, Illumina libraries were constructed with the Truseq Nano DNA library prep kit and sequenced using the Illumina HiSeq2500 platform at the Huntsman Cancer Institute of the University of Utah (Salt Lake City, UT, USA), generating paired-end reads of 125 bp. Genomic sequence reads of the four parental strains were publicly available in the NCBI Sequence Read Archive (SRA) under BioProject PRJNA799176 (Kurlovs et al, 2022). For all the experimental BSA replicates, Illumina libraries were constructed using the TruSeq Nano DNA sample preparation kit by Fasteris (https://www.fasteris.com/dna) and sequenced on an Illumina Novaseq 6000 Sequel platform, generating paired-end reads of 100 bp.…”

“…Most often, increased expression of these enzymes and transporters is associated with resistance, but the underlying gene regulatory mechanisms have in most cases remained elusive. Recently, the quantification of allele-specific expression was used to uncover that trans -driven gene regulation is common amongst detoxifying gene families such as P450s and DOGs in several resistant strains of the polyphagous arthropod Tetranychus urticae (Kurlovs et al, 2022). Yet, despite ample evidence on the proximal physiological processes and enzymatic pathways related to mechanisms of pesticide resistance in arthropods, the evolutionary origins of the underlying traits, the genetic structure, and the specific genomic targets of pesticide selection, as well as evidence for the synergism between different resistance mechanisms, are far from completely elucidated (Fotoukkiaii et al, 2021; Hawkins et al, 2018; Neve et al, 2014; Singh et al, 2021; Van Leeuwen & Dermauw, 2016).…”

“…In mites, transcriptional regulation could lead to the modular control and differential expression of groups of genes, and at least be partially responsible for some of the genes that are differentially expressed between parental lines. It was recently shown that especially P450s and DOGs are trans-regulated in some of these lines (Kurlovs et al, 2022). In addition, it has been shown that the P450 Cyp392A16 from T.…”