Disruption of a horizontally transferred phytoene desaturase abolishes carotenoid accumulation and diapause in Tetranychus urticae

Chromosome-level genome assembly of the two-spotted spider mite Tetranychus urticae

The two-spotted spider mite, Tetranychus urticae Koch (Acari: Tetranychidae), is a notorious pest in agriculture that has developed resistance to almost all chemical types used for its control. Here, we assembled a chromosome-level genome for the TSSM using Illumina, Nanopore, and Hi-C sequencing technologies. The assembled contigs had a total length of 103.94 Mb with an N50 of 3.46 Mb, with 87.7 Mb of 34 contigs anchored to three chromosomes. The chromosome-level genome assembly had a BUSCO completeness of 94.8%. We identified 15,604 protein-coding genes, with 11,435 genes that could be functionally annotated. The high-quality genome provides invaluable resources for the genetic and evolutionary study of TSSM.

SYNCAS: Efficient CRISPR/Cas9 gene-editing in difficult to transform arthropods

The genome editing technique CRISPR/Cas9 has led to major advancements in many research fields and this state-of-the-art tool has proven its use in genetic studies for various arthropods. However, most transformation protocols rely on microinjection of CRISPR/Cas9 components into embryos, a method which is challenging for many species. Alternatively, injections can be performed on adult females, but transformation efficiencies can be very low as was shown for the two-spotted spider mite, Tetranychus urticae, a minute but important chelicerate pest on many crops. In this study, we explored different CRISPR/Cas9 formulations to optimize a maternal injection protocol for T. urticae. We observed a strong synergy between branched amphipathic peptide capsules and saponins, resulting in a significant increase of CRISPR/Cas9 knock-out efficiency, exceeding 20%. This CRISPR/Cas9 formulation, termed SYNCAS, was used to knock-out different T. urticae genes - phytoene desaturase, CYP384A1 and Antennapedia - but also allowed to develop a co-CRISPR strategy and facilitated the generation of T. urticae knock-in mutants. In addition, SYNCAS was successfully applied to knock-out white and white-like genes in the western flower thrips, Frankliniella occidentalis. The SYNCAS method allows routine genome editing in these species and can be a game changer for genetic research in other hard to transform arthropods.

Contrasting roles of cytochrome P450s in amitraz and chlorfenapyr resistance in the crop pest Tetranychus urticae

The molecular mechanisms of amitraz and chlorfenapyr resistance remain only poorly understood for major agricultural pests and vectors of human diseases. This study focusses on a multi-resistant field strain of the crop pest Tetranychus urticae, which could be readily selected in the laboratory to high levels of amitraz and chlorfenapyr resistance. Toxicity experiments using tralopyril, the active toxophore of chlorfenapyr, suggested decreased activation as a likely mechanism underlying resistance. Starting from the same parental strain, transcriptome profiling revealed that a cluster of detoxifying genes was upregulated after amitraz selection, but unexpectedly downregulated after chlorfenapyr selection. Further functional validation associated the upregulation of CYP392A16 with amitraz metabolism and the downregulation of CYP392D8 with reduced activation of chlorfenapyr to tralopyril. Genetic mapping (QTL analysis by BSA) was conducted in an attempt to unravel the genetic mechanisms of expression variation and resistance. This revealed that chlorfenapyr resistance was associated with a single QTL, while 3 QTLs were uncovered for amitraz resistance. Together with the observed contrasting gene expression patterns, we argue that transcriptional regulators most likely underly the distinct expression profiles associated with resistance, but these await further functional validation.

Carotenoids: Distribution, Function in Nature, and Analysis Using LC-Photodiode Array Detector (DAD)-MS and MS/MS System

Carotenoids are tetraterpene pigments that are present in photosynthetic bacteria, some species of archaea and fungi, algae, plants, and animals. Carotenoids are essential pigments in photosynthetic organs along with chlorophylls. Carotenoids also act as photo-protectors, antioxidants, color attractants, and precursors of plant hormones in plants. Carotenoids in animals play important roles, such as precursors of vitamin A, photo-protectors, antioxidants, enhancers of immunity, and contributors to reproduction. More than 850 kinds of carotenoids are present in nature. The structures are similar and all of them are labile. Analysis of natural carotenoids requires the establishment of reliable methods for analyzing them. Liquid chromatography-mass spectrometry (LC-MS) and mass spectrometry/mass spectrometry (MS/MS) coupled with photodiode array detector (DAD) is an important tool for analysis of natural carotenoids. Electrospray ionization and atmospheric pressure chemical ionization are commonly used for ionization of LC-MS of carotenoids. MS and MS/MS provide not only molecular weight information but also some structural information on carotenoids. Ultraviolet-visible spectra from DAD provide information on chromophore systems, which cannot be provided by MS spectral data. In the present review, I report the structural diversity and function of natural carotenoids, and also describe the techniques for analysis of natural carotenoids using the LC-DAD-MS and MS/MS system.

Uridine Diphosphate Glycosyltransferases (UGTs) Involved in the Carotenoid-Based Body Color Difference between Tetranychus cinnabarinus (Red) and Tetranychus urticae (Green)

It has long been disputed whether Tetranychus cinnabarinus and Tetranychus urticae belong to the same genus, with T. cinnabarinus regarded as a red form of T. urticae. However, it is unclear why T. urticae and T. cinnabarinus have different body colors. Since carotenoids are responsible for the color of many organisms, the carotenoid profiles of T. cinnabarinus and T. urticae were compared by HPLC. There was no difference in carotenoid type, but T. cinnabarinus contained significantly more neoxanthin, astaxanthin, α-carotene, β-carotene, and γ-carotene, which may contribute to the deep red color. The transcriptome sequencing of both species identified 4079 differentially expressed genes (DEGs), of which 12 were related to carotenoid metabolism. RNA interference (RNAi) experiments demonstrated that silencing seven of these DEGs resulted in the different accumulation of carotenoid compounds in T. cinnabarinus and T. urticae. In addition, the body of T. urticae turned yellow after two days of feeding with UGT double-stranded RNAs and β-UGT small interfering RNAs. In conclusion, differences in the carotenoid profiles of T. urticae and T. cinnabarinus may be responsible for the different body colors.

Astaxanthin: Past, Present, and Future

Astaxanthin (AX), a lipid-soluble pigment belonging to the xanthophyll carotenoids family, has recently garnered significant attention due to its unique physical properties, biochemical attributes, and physiological effects. Originally recognized primarily for its role in imparting the characteristic red-pink color to various organisms, AX is currently experiencing a surge in interest and research. The growing body of literature in this field predominantly focuses on AXs distinctive bioactivities and properties. However, the potential of algae-derived AX as a solution to various global environmental and societal challenges that threaten life on our planet has not received extensive attention. Furthermore, the historical context and the role of AX in nature, as well as its significance in diverse cultures and traditional health practices, have not been comprehensively explored in previous works. This review article embarks on a comprehensive journey through the history leading up to the present, offering insights into the discovery of AX, its chemical and physical attributes, distribution in organisms, and biosynthesis. Additionally, it delves into the intricate realm of health benefits, biofunctional characteristics, and the current market status of AX. By encompassing these multifaceted aspects, this review aims to provide readers with a more profound understanding and a robust foundation for future scientific endeavors directed at addressing societal needs for sustainable nutritional and medicinal solutions. An updated summary of AXs health benefits, its present market status, and potential future applications are also included for a well-rounded perspective.

A nuclear receptor HR96-related gene underlies large trans-driven differences in detoxification gene expression in a generalist herbivore

The role, magnitude, and molecular nature of trans-driven expression variation underlying the upregulation of detoxification genes in pesticide resistant arthropod populations has remained enigmatic. In this study, we performed expression quantitative trait locus (eQTL) mapping (n = 458) between a pesticide resistant and a susceptible strain of the generalist herbivore and crop pest Tetranychus urticae. We found that a single trans eQTL hotspot controlled large differences in the expression of a subset of genes in different detoxification gene families, as well as other genes associated with host plant use. As established by additional genetic approaches including RNAi gene knockdown, a duplicated gene with a nuclear hormone receptor HR96-related ligand-binding domain was identified as causal for the expression differences between strains. The presence of a large family of HR96-related genes in T. urticae may enable modular control of detoxification and host plant use genes, facilitating this species' known and rapid evolution to diverse pesticides and host plants.

The chigger microbiome: big questions in a tiny world

'Chiggers' (trombiculid mite larvae) are best known as vectors of rickettsial pathogens, Orientia spp., which cause a zoonosis, scrub typhus. However, several other pathogens (e.g., Hantaan orthohantavirus, Dabie bandavirus, Anaplasma spp., Bartonella spp., Borrelia spp., and Rickettsia spp.) and bacterial symbionts (e.g., Cardinium, Rickettsiella, and Wolbachia) are being reported from chiggers with increasing frequency. Here, we explore the surprisingly diverse chigger microbiota and potential interactions within this microcosm. Key conclusions include a possible role for chiggers as vectors of viral diseases; the dominance in some chigger populations of unidentified symbionts in several bacterial families; and increasing evidence for vertical transmission of potential pathogens and symbiotic bacteria in chiggers, suggesting intimate interactions and not simply incidental acquisition of bacteria from the environment or host.

Rop plays conserved roles in the reproductive and digestive processes of spider mites

Ras opposite (Rop) is known to play an essential role in regulating vesicle trafficking, including synaptic transmission and general secretion. The fundamental roles of Rop have been confirmed by the observation that null mutations in many organisms generate lethal phenotypes during embryogenesis. However, the effects of Rop during the postembryonic stages, especially in non-model organisms, remain largely unknown. Here, we provide new data that enhance our understanding of Rop's roles in the adults of multiple species of Tetranychus spider mites (Acari: Tetranychidae), a class of notorious agricultural pests. Our in silico and experimental evidence demonstrated that Rop is under purifying selection and is highly conserved in Tetranychus spp. RNA interference experiments showed that Rop is required for maintaining normal fecundity but has no significant effect on survival. We further demonstrate that knockdown of Rop darkens the body color of spider mites and blocks the excretion of fecal pellets, which is likely to be related to an abnormality in the excretion of food waste in the digestive system. Overall, our findings clarify novel functions of a vesicle trafficking-related gene in the adult stage of multiple Tetranychus species and highlight the need to evaluate the roles of essential genes in various organisms.

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

Pesticide resistance relies on a myriad of mechanisms, ranging from single mutations to a complex and polygenic architecture, and it involves mechanisms such as target-site insensitivity, metabolic detoxification, or a combination of these, with either additive or synergistic effects. Several resistance mechanisms against abamectin, a macrocyclic lactone widely used in crop protection, have been reported in the cosmopolitan pest Tetranychus urticae. However, it has been shown that a single mechanism cannot account for the high levels of abamectin resistance found across different mite populations. Here, we used experimental evolution combined with bulked segregant analyses to map quantitative trait loci (QTL) associated with abamectin resistance in two genetically unrelated populations of T. urticae. In these two independent QTL mapping experiments, three and four QTLs were identified, of which three were shared between experiments. Shared QTLs contained genes encoding subunits of the glutamate-gated chloride channel (GluCl) and harboured previously reported mutations, including G314D in GluCl1 and G326E in GluCl3, but also novel resistance candidate loci, including DNA helicases and chemosensory receptors. Surprisingly, the fourth QTL, present only in only one of the experiments and thus unique for one resistant parental line, revealed a non-functional variant of GluCl2, suggesting gene knock-out as resistance mechanism. Our study uncovers the complex basis of abamectin resistance, and it highlights the intraspecific diversity of genetic mechanisms underlying resistance in a cosmopolitan pest.

Horizontal Gene Transfer and Fusion Spread Carotenogenesis Among Diverse Heterotrophic Protists

Thraustochytrids (phylum: Labyrinthulomycota) are nonphotosynthetic marine protists. Some thraustochytrids have crtIBY, a trifunctional fusion gene encoding a protein capable of β-carotene biosynthesis from geranylgeranyl pyrophosphate. Here we show that crtIBY is essential in, and encodes the sole pathway for, carotenoid biosynthesis in the thraustochytrid Aurantiochytrium limacinum ATCC MYA-1381. We explore the evolutionary origins of CrtIBY and discover that the closest related protein domains are present in a small but diverse group of other heterotrophic protists, including the apusomonad Thecamonas trahens and the dinoflagellates Oxyrrhis marina and Noctiluca scintillans. Each organism within this cluster also contains one or more β-carotene 15-15' oxygenase genes (blh and rpe65), suggesting that the acquisition of β-carotene biosynthesis genes may have been related to the production of retinal. Our findings support a novel origin of eukaryotic (apo)carotenoid biosynthesis by horizontal gene transfer from Actinobacteria, Bacteroidetes, and/or Archaea. This reveals a remarkable case of parallel evolution of eukaryotic (apo)carotenogenesis in divergent protistan lineages by repeated gene transfers.

Juvenile hormone regulates the photoperiodic plasticity of elytra coloration in the ladybird Harmonia axyridis

Many animals, including insects, exhibit plasticity of body colour in response to environmental changes. Varied expression of carotenoids, major cuticle pigments, significantly contributes to body colour flexibility. However, the molecular mechanisms by which environmental cues regulate carotenoid expression remain largely unknown. In this study, we used the ladybird Harmonia axyridis as a model to investigate the photoperiodic-responsive plasticity of elytra coloration and its endocrine regulation. It was found that H. axyridis females under long-day conditions develop elytra that are much redder than those under short-day conditions, resulting from the differential accumulation of carotenoids. Exogenous hormone application and RNAi-mediated gene knockdown indicate that carotenoid deposition was directed through the juvenile hormone (JH) receptor-mediated canonical pathway. Moreover, we characterized an SR-BI/CD36 (SCRB) gene SCRB10 as the carotenoid transporter responding to JH signalling and regulating the elytra coloration plasticity. Taken together, we propose that JH signalling transcriptionally regulates the carotenoid transporter gene for the photoperiodic coloration plasticity of elytra in the beetles, which reveals a novel role of the endocrine system in the regulation of carotenoid-associated animal body coloration under environmental stimuli.

Biology of Two-Spotted Spider Mite (Tetranychus urticae): Ultrastructure, Photosynthesis, Guanine Transcriptomics, Carotenoids and Chlorophylls Metabolism, and Decoyinine as a Potential Acaricide

Two-Spotted Spider Mites (TSSMs, Tetranychus urticae Koch 1836 (Acari: Tetranychidae)) is one of the most important pests in many crop plants, and their feeding activity is based on sucking leaf cell contents. The purpose of this study was to evaluate the interaction between TSSMs and their host Lima bean (Phaseolus lunatus) by analyzing the metabolomics of leaf pigments and the transcriptomics of TSSM guanine production. We also used epifluorescence, confocal laser scanning, and transmission electron microscopies to study the morphology and structure of TSSMs and their excreta. Finally, we evaluated the potential photosynthetic ability of TSSMs and the activity and content of Ribulose-1,5-bisphosphate Carboxylase/Oxigenase (RubisCO). We found that TSSMs express several genes involved in guanine production, including Guanosine Monophosphate Synthetase (GMPS) and decoyinine (DCY), a potential inhibitor of GMPS, was found to reduce TSSMs proliferation in infested Lima bean leaves. Despite the presence of intact chloroplasts and chlorophyll in TSSMs, we demonstrate that TSSMs do not retain any photosynthetic activity. Our results show for the first time the transcriptomics of guanine production in TSSMs and provide new insight into the catabolic activity of TSSMs on leaf chlorophyll and carotenoids. Finally, we preliminary demonstrate that DCY has an acaricidal potential against TSSMs.

The flashy red color of the red velvet mite Balaustium murorum (Prostigmata: Erythraeidae) is caused by high abundance of the keto-carotenoids, astaxanthin and 3-hydroxyechinenone

The red velvet mite, Balaustium murorum (Hermann), is a pollenophagous free-living mite with a flashy red body. This mite occurs in early spring and lives on sunny surfaces of human-made structures, such as concrete. Hence, it is inevitably exposed to a harsh environment due to solar ultraviolet-B (UV-B) radiation and radiant heat, which cause oxidative stress via the production of reactive oxygen species. The spider mite Panonychus citri that resides on upper leaf surfaces accumulates synthesized keto-carotenoids to protect against oxidative stress. Therefore, we evaluated carotenoid composition in the red pigment of B. murorum. To identify major carotenoids, we performed a high-performance liquid chromatography analysis of intact and de-esterified pigments of B. murorum females. The flashy red pigments of B. murorum consisted of the highly abundant keto-carotenoids astaxanthin and 3-hydroxyechinenone (60 and 38% of major carotenoids, respectively), and a small amount of β-carotene (2%). Although P. citri is an astaxanthin-rich species, the astaxanthin concentration (per protein) in B. murorum is 127-fold that in P. citri. Due to their high antioxidant activities, those keto-carotenoids probably contribute to the survival of B. murorum in the harsh environment caused by solar UV-B radiation and radiant heat in inorganic habitats.

Trans-driven variation in expression is common among detoxification genes in the extreme generalist herbivore Tetranychus urticae

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.

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

Pyrethroids are widely applied insecticides in agriculture, but their frequent use has provoked many cases of resistance, in which mutations in the voltage-gated sodium channel (VGSC), the pyrethroid target-site, were shown to play a major role. However, for the spider mite Tetranychus urticae, it has also been shown that increased detoxification contributes to resistance against the pyrethroid bifenthrin. Here, we performed QTL-mapping to identify the genomic loci underlying bifenthrin resistance in T. urticae. Two loci on chromosome 1 were identified, with the VGSC gene being located near the second QTL and harboring the well-known L1024V mutation. In addition, the presence of an L925M mutation in the VGSC of a highly bifenthrin-resistant strain and its loss in its derived, susceptible, inbred line indicated the importance of target-site mutations in bifenthrin resistance. Further, RNAseq experiments revealed that genes encoding detoxification enzymes, including carboxyl/choline esterases (CCEs), cytochrome P450 monooxygenases and UDP-glycosyl transferases (UGTs), were overexpressed in resistant strains. Toxicity bioassays with bifenthrin (ester pyrethroid) and etofenprox (non-ester pyrethroid) also indicated a possible role for CCEs in bifenthrin resistance. A selection of CCEs and UGTs were therefore functionally expressed, and CCEinc18 was shown to metabolize bifenthrin, while teturUGT10 could glycosylate bifenthrin-alcohol. To conclude, our findings suggest that both target-site and metabolic mechanisms underlie bifenthrin resistance in T. urticae, and these might synergize high levels of resistance.

Circadian and Neuroendocrine Basis of Photoperiodism Controlling Diapause in Insects and Mites: A Review

The photoperiodic system is concealed in the highly complex black-box, comprising four functional subunits: 1) a photo/thermo-sensitive input unit, 2) a photoperiodic clock based on a circadian system, 3) a condenser unit counting the number of inductive signals, and 4) a neuroendocrine switch that triggers a phenotypic shift. This review aims to summarize the research history and current reach of our understanding on this subject to connect it with the molecular mechanism of the circadian clock rapidly being unveiled. The review also focuses on the mode of intersubunit information transduction. It will scan the recent advancement in research on each functional subunit, but special attention will be given to the circadian clock-endocrine conjunct and the role of melatonin signaling in the regulation of insect photoperiodism. Prothoracicotropic hormone (PTTH) probably plays the most crucial role in the regulation of pupal diapause, which is the simplest model system of diapause regulation by hormones investigated so far, particularly in the Chinese oak silkmoth (Antheraea pernyi). A search for the trigger to release the PTTH found some candidates, that is, indoleamines. Indolamine metabolism is controlled by arylalkylamine N-acetyltransferase (aaNAT). Indolamine dynamics and aaNAT enzymatic activity changed according to photoperiods. aaNAT activity and melatonin content in the brain showed not only a photoperiodic response but also a circadian fluctuation. aaNAT had multiple E-boxes, suggesting that it is a clock-controlled gene (ccg), which implies that cycle (cyc, or brain-muscle Arnt-like 1 = Bmal1)/Clock (Clk) heterodimer binds to E-box and stimulates the transcription of aaNAT, which causes the synthesis of melatonin. RNAi against transcription modulators, cyc, or Clk downregulated aaNAT transcription, while RNAi against repressor of cyc/Clk, per upregulated aaNAT transcription. Immunohistochemical localization showed that the circadian neurons carry epitopes of melatonin-producing elements such as aaNAT, the precursor serotonin, HIOMT, and melatonin as well as clock gene products such as cyc-ir, Per-ir, and dbt-ir, while PTTH-producing neurons juxtaposed against the clock neurons showed hMT2-ir in A. pernyi brain. Melatonin probably binds to the putative melatonin receptor (MT) that stimulates Ca2+ influx, which in turn activates PKC. This induces Rab 8 phosphorylation and exocytosis of PTTH, leading to termination of diapause. All the PTTH-expressing neurons have PKC-ir, and Rab8-ir. When diapause is induced and maintained under short days, serotonin binding to 5HTR1B suppresses PTTH release in a yet unknown way. RNAi against this receptor knocked out photoperiodism; short day response is blocked and diapause was terminated even under the short day condition. The result showed that a relatively simple system controls both induction and termination in pupal diapause of A. pernyi: the circadian system regulates the transcription of aaNAT as a binary switch, the enzyme produces a melatonin rhythm that gates PTTH release, and 5HTR1B and MT are probably also under photoperiodic regulation. Finally, we listed the remaining riddles which need to be resolved, to fully understand this highly complex system in future studies.

Intradiol ring cleavage dioxygenases from herbivorous spider mites as a new detoxification enzyme family in animals

Background

Generalist herbivores such as the two-spotted spider mite Tetranychus urticae thrive on a wide variety of plants and can rapidly adapt to novel hosts. What traits enable polyphagous herbivores to cope with the diversity of secondary metabolites in their variable plant diet is unclear. Genome sequencing of T. urticae revealed the presence of 17 genes that code for secreted proteins with strong homology to “intradiol ring cleavage dioxygenases (DOGs)” from bacteria and fungi, and phylogenetic analyses show that they have been acquired by horizontal gene transfer from fungi. In bacteria and fungi, DOGs have been well characterized and cleave aromatic rings in catecholic compounds between adjacent hydroxyl groups. Such compounds are found in high amounts in solanaceous plants like tomato, where they protect against herbivory. To better understand the role of this gene family in spider mites, we used a multi-disciplinary approach to functionally characterize the various T. urticae DOG genes.

Results

We confirmed that DOG genes were present in the T. urticae genome and performed a phylogenetic reconstruction using transcriptomic and genomic data to advance our understanding of the evolutionary history of spider mite DOG genes. We found that DOG expression differed between mites from different plant hosts and was induced in response to jasmonic acid defense signaling. In consonance with a presumed role in detoxification, expression was localized in the mite’s gut region. Silencing selected DOGs expression by dsRNA injection reduced the mites’ survival rate on tomato, further supporting a role in mitigating the plant defense response. Recombinant purified DOGs displayed a broad substrate promiscuity, cleaving a surprisingly wide array of aromatic plant metabolites, greatly exceeding the metabolic capacity of previously characterized microbial DOGs.

Conclusion

Our findings suggest that the laterally acquired spider mite DOGs function as detoxification enzymes in the gut, disarming plant metabolites before they reach toxic levels. We provide experimental evidence to support the hypothesis that this proliferated gene family in T. urticae is causally linked to its ability to feed on an extremely wide range of host plants.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12915-022-01323-1.

Characterization of carotenoid biosynthetic pathway genes in the pea aphid (Acyrthosiphon pisum) revealed by heterologous complementation and RNA interference assays

Carotenoids are involved in many essential physiological functions and are produced from geranylgeranyl pyrophosphate through synthase, desaturase, and cyclase activities. In the pea aphid (Acyrthosiphon pisum), the duplication of carotenoid biosynthetic genes, including carotenoid synthases/cyclases (ApCscA-C) and desaturases (ApCdeA-D), through horizontal gene transfer from fungi has been detected, and ApCdeB has known dehydrogenation functions. However, whether other genes contribute to aphid carotenoid biosynthesis, and its specific regulatory pathway, remains unclear. In the current study, functional analyses of seven genes were performed using heterologous complementation and RNA interference assays. The bifunctional enzymes ApCscA-C were responsible for the synthase of phytoene, and ApCscC may also have a cyclase activity. ApCdeA, ApCdeC, and ApCdeD had diverse dehydrogenation functions. ApCdeA catalyzed the enzymatic conversion of phytoene to neurosporene (three-step product), ApCdeC catalyzed the enzymatic conversion of phytoene to ζ-carotene (two-step product), and ApCdeD catalyzed the enzymatic conversion of phytoene to lycopene (four-step product). Silencing of ApCscs reduced the expression levels of ApCdes, and silencing these carotenoid biosynthetic genes reduced the α-, β-, and γ-carotene levels, as well as the total carotenoid level. The results suggest that these genes were activated and led to carotenoid biosynthesis in the pea aphid.

QTL mapping suggests that both cytochrome P450-mediated detoxification and target-site resistance are involved in fenbutatin oxide resistance in Tetranychus urticae

The organotin acaricide fenbutatin oxide (FBO) - an inhibitor of mitochondrial ATP-synthase - has been one of the most extensively used acaricides for the control of spider mites, and is still in use today. Resistance against FBO has evolved in many regions around the world but only few studies have investigated the molecular and genetic mechanisms of resistance to organotin acaricides. Here, we found that FBO resistance is polygenic in two genetically distant, highly resistant strains of the spider mite Tetranychus urticae, MAR-AB and MR-VL. To identify the loci underlying FBO resistance, two independent bulked segregant analysis (BSA) based QTL mapping experiments, BSA MAR-AB and BSA MR-VL, were performed. Two QTLs on chromosome 1 were associated with FBO resistance in each mapping experiment. At the second QTL of BSA MAR-AB, several cytochrome P450 monooxygenase (CYP) genes were located, including CYP392E4, CYP392E6 and CYP392E11, the latter being overexpressed in MAR-AB. Synergism tests further implied a role for CYPs in FBO resistance. Subunit c of mitochondrial ATP-synthase was located near the first QTL of both mapping experiments and harbored a unique V89A mutation enriched in the resistant parents and selected BSA populations. Marker-assisted introgression into a susceptible strain demonstrated a moderate but significant effect of the V89A mutation on toxicity of organotin acaricides. The impact of the mutation on organotin inhibition of ATP synthase was also functionally confirmed by ATPase assays on mitochondrial preparations. To conclude, our findings suggest that FBO resistance in the spider mite T. urticae is a complex interplay between CYP-mediated detoxification and target-site resistance.

Insights into gene manipulation techniques for Acari functional genomics

Functional genomics is an essential tool for elucidating the structure and function of genes in any living organism. Here, we review the use of different gene manipulation techniques in functional genomics of Acari (mites and ticks). Some of these Acari species inflict severe economic losses to managed crops and health problems to humans, wild and domestic animals, but many also provide important ecosystem services worldwide. Currently, RNA interference (RNAi) is the leading gene expression manipulation tool followed by gene editing via the bacterial type II Clustered Regularly Interspaced Short Palindromic Repeats and associated protein 9 system (CRISPR-Cas9). Whilst RNAi, via siRNA, does not always lead to expected outcomes, the exploitations of the CRISPR systems in Acari are still in their infancy and are limited only to CRISP/Cas9 to date. In this review, we discuss the advantages and disadvantages of RNAi and CRISPR-Cas9 and the technical challenges associated with their exploitations. We also compare the biochemical machinery of RNAi and CRISPR-Cas9 technologies. We highlight some potential solutions for experimental optimization of each mechanism in gene function studies. The potential benefits of adopting various CRISPR-Cas9 systems for expanding on functional genomics experiments in Acari are also discussed.

Predicting the genomic resolution of bulk segregant analysis

Bulk segregant analysis is a technique for identifying the genetic loci that underlie phenotypic trait differences. The basic approach is to compare two pools of individuals from the opposing tails of the phenotypic distribution, sampled from an interbred population. Each pool is sequenced and scanned for alleles that show divergent frequencies between the pools, indicating potential association with the observed trait differences. Bulk segregant analysis has already been successfully applied to the mapping of various quantitative trait loci in organisms ranging from yeast to maize. However, these studies have typically suffered from rather low mapping resolution, and we still lack a detailed understanding of how this resolution is affected by experimental parameters. Here, we use coalescence theory to calculate the expected genomic resolution of bulk segregant analysis for a simple monogenic trait. We first show that in an idealized interbreeding population of infinite size, the expected length of the mapped region is inversely proportional to the recombination rate, the number of generations of interbreeding, and the number of genomes sampled, as intuitively expected. In a finite population, coalescence events in the genealogy of the sample reduce the number of potentially informative recombination events during interbreeding, thereby increasing the length of the mapped region. This is incorporated into our model by an effective population size parameter that specifies the pairwise coalescence rate of the interbreeding population. The mapping resolution predicted by our calculations closely matches numerical simulations and is surprisingly robust to moderate levels of contamination of the segregant pools with alternative alleles. Furthermore, we show that the approach can easily be extended to modifications of the crossing scheme. Our framework will allow researchers to predict the expected power of their mapping experiments, and to evaluate how their experimental design could be tuned to optimize mapping resolution.

Over-expression in cis of the midgut P450 CYP392A16 contributes to abamectin resistance in Tetranychus urticae

Cytochrome P450 mediated metabolism is a well-known mechanism of insecticide resistance. However, to what extent qualitative or quantitative changes are responsible for increased metabolism, is not well understood. Increased expression of P450 genes is most often reported, but the underlying regulatory mechanisms remain widely unclear. In this study, we investigate CYP392A16, a P450 from the polyphagous and major agricultural pest Tetranychus urticae. High expression levels of CYP392A16 and in vitro metabolism assays have previously associated this P450 with abamectin resistance. Here, we show that CYP392A16 is primarily localized in the midgut epithelial cells, as indicated by immunofluorescence analysis, a finding also supported by a comparison between feeding and contact toxicity bioassays. Silencing via RNAi of CYP392A16 in a highly resistant T. urticae population reduced insecticide resistance levels from 3400- to 1900- fold, compared to the susceptible reference strain. Marker-assisted backcrossing, using a single nucleotide polymorphism (SNP) found in the CYP392A16 allele from the resistant population, was subsequently performed to create congenic lines bearing this gene in a susceptible genetic background. Toxicity assays indicated that the allele derived from the resistant strain confers 3.6-fold abamectin resistance compared to the lines with susceptible genetic background. CYP392A16 is over-expressed at the same levels in these lines, pointing to cis-regulation of gene expression. In support of that, functional analysis of the putative promoter region from the resistant and susceptible parental strains revealed a higher reporter gene expression, confirming the presence of cis-acting regulatory mechanisms.

The potential pigmentation-related genes in spider mites revealed by comparative transcriptomes of the red form of Tetranychus urticae

Colouration in spider mites is due to the presence of carotenoids with diverse colours, including yellows, oranges and reds. Tetranychus urticae has two main colour forms, red and green. Although a ketolase has been implicated in determining the colour, the underlying genetic basis of body colour divergence between the two forms has remained unclear. Based on a combination of comparative transcriptomes and RNA interference, we found that a gene encoding a cytochrome P450 enzyme of the CYP4 clan (CYP389B1) had remarkably high expression in adult females of the red T. urticae, as well as in hybrids obtained by crossing the red and green forms. Down-regulation of this gene by RNA interference resulted in decreased accumulation of red pigment. Up-regulation of the expressions of a scavenger receptor gene (SCARB1) and a mitochondrial glycine transporter (SLC25A38) also strongly contributed to red colour development in adult females. Suppressing the mRNA levels of these genes also resulted in reduced accumulation of red pigment in the three other spider mites with red body colour. Our results provide evidence that the body colour divergence between the two forms is caused by different expressions of pigmentation-related genes, and point to a possible role of a novel cytochrome P450 gene (CYP389B1) in regulating red-orange body colour. These findings expand the number of candidate cytochrome P450 genes involved in endogenous pigmentation and will help to understand their roles in determining colour patterns in mites and other species.

Comparing the efficiency of RNAi after feeding and injection of dsRNA in spider mites

Pesticide resistance in spider mites drives the development of acaricides with novel mode of action, which could benefit from RNAi as a screening tool in search of new molecular targets. RNAi via oral delivery of dsRNA has been frequently reported in spider mites, but injection of dsRNA is rarely reported. We compare here the efficiency of oral delivery versus injection of dsRNA in female adult mites. When comparing silencing efficiency, oral delivery of dsRNAs silenced 40.6 ± 8.9% of CPR, 63.8 ± 6.9% of CHMP2A, and 37.7 ± 5.7% of CHMP3 genes. Similar silencing efficiencies were found for injection (48.6 ± 3.7% of CPR, 70.2 ± 4.1% of CHMP2A, 59.8 ± 2.2% of CHMP3), but with much lower quantities of dsRNAs. Oral delivery of dsRNA failed to silence the expression of the CHMP4B gene, but this could be accomplished by injection of dsRNA (23.1 ± 1.0%). When scoring the phenotypic effects of silencing, both oral delivery and injection of CHMP2A- and CHMP3-dsRNA influenced the locomotion speed of mites significantly. For CPR, silencing could only be accomplished by dsRNA injection, not by feeding. CPR silencing significantly impacted the toxicity of a typical acaricide, pyridaben, as the susceptibility of mites raised 2.75-fold. Last, injection of Eya-dsRNA in adults produced transgenerational phenotypic effects on 3.59% of offspring, as quantified by an observed deviation in eye development, while oral delivery of Eya-dsRNA did not. In conclusion, injection of dsRNA is superior to oral delivery in silencing the expression of the selected genes in this study and could be considered the method of choice to study gene function in reverse genetic approaches.

Strategies to meet the global demand for natural food colorant bixin: A multidisciplinary approach

Bixin is an apocarotenoid derived from Bixa orellana L. well known as a food colorant along with its numerous industrial and therapeutic applications. With the current surge in usage of natural products, bixin has contributed immensely to the world carotenoid market and showcases a spike in its requirement globally. To bridge the gap between bixin availability and utility, owed to its bioactivity and demand as a colouring agent in industries the sustainable production of bixin is critical. Therefore, to meet up this challenge effective use of multidisciplinary strategies is a promising choice to enhance bixin quantity and quality. Here we report, an optimal blend of approaches directed towards manipulation of bixin biosynthesis pathway with an insight into the impact of regulatory mechanisms and environmental dynamics, engineering carotenoid degradation in plants other than annatto, usage of tissue culture techniques supported with diverse elicitations, molecular breeding, application of in silico predictive tools, screening of microbial bio-factories as alternatives, preservation of bixin bioavailability, and promotion of eco-friendly extraction techniques to play a collaborative role in promoting sustainable bixin production.

Maize Inbred Line B96 Is the Source of Large-Effect Loci for Resistance to Generalist but Not Specialist Spider Mites

Maize (Zea mays subsp. mays) yield loss from arthropod herbivory is substantial. While the basis of resistance to major insect herbivores has been comparatively well-studied in maize, less is known about resistance to spider mite herbivores, which are distantly related to insects and feed by a different mechanism. Two spider mites, the generalist Tetranychus urticae, and the grass-specialist Oligonychus pratensis, are notable pests of maize, especially during drought conditions. We assessed resistance (antibiosis) to both mites of 38 highly diverse maize lines, including several previously reported to be resistant to one or the other mite species. We found that line B96, as well as its derivatives B49 and B75, were highly resistant to T. urticae. In contrast, neither these three lines, nor any others included in our study, were notably resistant to the specialist O. pratensis. Quantitative trait locus (QTL) mapping with replicate populations from crosses of B49, B75, and B96 to susceptible B73 identified a QTL in the same genomic interval on chromosome 6 for T. urticae resistance in each of the three resistant lines, and an additional resistance QTL on chromosome 1 was unique to B96. Single-locus genotyping with a marker coincident with the chromosome 6 QTL in crosses of both B49 and B75 to B73 revealed that the respective QTL was large-effect; it explained ∼70% of the variance in resistance, and resistance alleles from B49 and B75 acted recessively as compared to B73. Finally, a genome-wide haplotype analysis using genome sequence data generated for B49, B75, and B96 identified an identical haplotype, likely of initial origin from B96, as the source of T. urticae resistance on chromosome 6 in each of the B49, B75, and B96 lines. Our findings uncover the relationship between intraspecific variation in maize defenses and resistance to its major generalist and specialist spider mite herbivores, and we identified loci for use in breeding programs and for genetic studies of resistance to T. urticae, the most widespread spider mite pest of maize.

High-resolution genetic mapping reveals cis-regulatory and copy number variation in loci associated with cytochrome P450-mediated detoxification in a generalist arthropod pest

Chemical control strategies are driving the evolution of pesticide resistance in pest populations. Understanding the genetic mechanisms of these evolutionary processes is of crucial importance to develop sustainable resistance management strategies. The acaricide pyflubumide is one of the most recently developed mitochondrial complex II inhibitors with a new mode of action that specifically targets spider mite pests. In this study, we characterize the molecular basis of pyflubumide resistance in a highly resistant population of the spider mite Tetranychus urticae. Classical genetic crosses indicated that pyflubumide resistance was incompletely recessive and controlled by more than one gene. To identify resistance loci, we crossed the resistant population to a highly susceptible T. urticae inbred strain and propagated resulting populations with and without pyflubumide exposure for multiple generations in an experimental evolution set-up. High-resolution genetic mapping by a bulked segregant analysis approach led to the identification of three quantitative trait loci (QTL) linked to pyflubumide resistance. Two QTLs were found on the first chromosome and centered on the cytochrome P450 CYP392A16 and a cluster of CYP392E6-8 genes. Comparative transcriptomics revealed a consistent overexpression of CYP392A16 and CYP392E8 in the experimental populations that were selected for pyflubumide resistance. We further corroborated the involvement of CYP392A16 in resistance by in vitro functional expression and metabolism studies. Collectively, these experiments uncovered that CYP392A16 N-demethylates the toxic carboxamide form of pyflubumide to a non-toxic compound. A third QTL coincided with cytochrome P450 reductase (CPR), a vital component of cytochrome P450 metabolism. We show here that the resistant population harbors three gene copies of CPR and that this copy number variation is associated with higher mRNA abundance. Together, we provide evidence for detoxification of pyflubumide by cytochrome P450s that is likely synergized by gene amplification of CPR.

Our understanding of the causal genetic variants that drive the evolution of quantitative traits, such as polygenic pesticide resistance, remains very limited. Here, we followed a high-resolution genetic mapping approach to localize the genetic variants that cause pyflubumide resistance in the two-spotted spider mite Tetranychus urticae. Three well-supported QTL were uncovered and pointed towards a major role for cytochrome P450-mediated detoxification. Cis-regulatory variation for cytochrome P450s was observed, and in vitro cytochrome P450 experiments showed that pyflubumide was metabolized into a non-toxic derivate. A third QTL centered on cytochrome P450 reductase (CPR), which is required for cytochrome P450 activity, and is amplified in pyflubumide resistant populations. Our results indicate that pyflubumide resistance is mediated by cytochrome P450 detoxification that is enhanced by gene amplification at the CPR locus.

Elucidation of the whole carotenoid biosynthetic pathway of aphids at the gene level and arthropodal food chain involving aphids and the red dragonfly

Background

Aphids can be positioned as robust pest insects in farming and as ones of the model organisms for arthropods in molecular biology. Carotenoids are pigments that protect organisms from photooxidative damage caused by excessive light. Aphids were shown to possess genes of fungal origin for carotenoid biosynthesis, whereas a little knowledge was available about the functions of the genes and the biosynthetic pathway. Even carotenoid species contained in aphids were not enough understood. Main purpose of this study is to clarify these insufficient findings.

Results

The whole carotenoid biosynthetic pathway of the pea aphid (Acyrthosiphon pisum) was elucidated at the gene level, through comprehensive functional analysis of its carotenogenic genes, using Escherichia coli that synthesized carotenoid substrates, along with structural and quantitative analysis of carotenoids from various aphid species. Four genes were needed to synthesize all carotenoids accumulated in aphids from geranylgeranyl diphosphate. The tor gene mediated desaturation reaction from phytoene to 3,4-didehydrolycopene. It was revealed that a gene designated ApCrtYB3, which was considered to have functionally evolved in aphids, can convert lycopene into uncommon carotenoids with the γ-ring such as (6′S)-β,γ-carotene and γ,γ-carotene. We further demonstrated that the atypical carotenoids work as ecological indicators for estimating the food chain from aphids to predatory arthropods, and showed that aphids contributed with significant levels to the food chain from insect herbivores to several predatory arthropods, i.e., the red dragonfly (Sympetrum frequens; adults), seven-spotted ladybird (Coccinella septempunctata), and two spiders, Oxyopes sertatus and Nephila clavata. Gut microflora of the dragonfly (mature adults) was also found to include endosymbiotic bacteria such as Serratia symbiotica specific to the black bean aphid (Aphis fabae).

Conclusions

We revealed the whole carotenoid biosynthetic pathway of aphids, including functional identification of the corresponding genes. Subsequently, we showed that arthropodal food chain can be estimated using the uncommon carotenoids of aphids as ecological indicators. This result indicated that aphids made significant contributions to the food chain of several predatory arthropods including the red-dragonfly adults. Aphids are likely to be positioned as an important “phytochemicals” source for some predatory insects and arachnids, which are often active under bright sunlight.

Genetic Manipulation of Ticks: A Paradigm Shift in Tick and Tick-Borne Diseases Research

Ticks are obligate hematophagous arthropods that are distributed worldwide and are one of the most important vectors of pathogens affecting humans and animals. Despite the growing burden of tick-borne diseases, research on ticks has lagged behind other arthropod vectors, such as mosquitoes. This is largely because of challenges in applying functional genomics and genetic tools to the idiosyncrasies unique to tick biology, particularly techniques for stable genetic transformations. CRISPR-Cas9 is transforming non-model organism research; however, successful germline editing has yet to be accomplished in ticks. Here, we review the ancillary methods needed for transgenic tick development and the use of CRISPR/Cas9, the most promising gene-editing approach, for tick genetic transformation.

A complete enzymatic capacity for biosynthesis of docosahexaenoic acid (DHA, 22 : 6n-3) exists in the marine Harpacticoida copepod Tigriopus californicus

The long-standing paradigm establishing that global production of Omega-3 (n–3) long-chain polyunsaturated fatty acids (LC-PUFA) derived almost exclusively from marine single-cell organisms, was recently challenged by the discovery that multiple invertebrates possess methyl-end (or ωx) desaturases, critical enzymes enabling the biosynthesis of n–3 LC-PUFA. However, the question of whether animals with ωx desaturases have complete n–3 LC-PUFA biosynthetic pathways and hence can contribute to the production of these compounds in marine ecosystems remained unanswered. In the present study, we investigated the complete enzymatic complement involved in the n–3 LC-PUFA biosynthesis in Tigriopus californicus, an intertidal harpacticoid copepod. A total of two ωx desaturases, five front-end desaturases and six fatty acyl elongases were successfully isolated and functionally characterized. The T. californicus ωx desaturases enable the de novo biosynthesis of C₁₈ PUFA such as linoleic and α-linolenic acids, as well as several n–3 LC-PUFA from n–6 substrates. Functions demonstrated in front-end desaturases and fatty acyl elongases unveiled various routes through which T. californicus can biosynthesize the physiologically important arachidonic and eicosapentaenoic acids. Moreover, T. californicus possess a Δ4 desaturase, enabling the biosynthesis of docosahexaenoic acid via the ‘Δ4 pathway’. In conclusion, harpacticoid copepods such as T. californicus have complete n–3 LC-PUFA biosynthetic pathways and such capacity illustrates major roles of these invertebrates in the provision of essential fatty acids to upper trophic levels.

Untangling a Gordian knot: the role of a GluCl3 I321T mutation in abamectin resistance in Tetranychus urticae

BACKGROUND

The cys-loop ligand-gated ion channels, including the glutamate-gated chloride channel (GluCl) and GABA-gated chloride channel (Rdl) are important targets for drugs and pesticides. The macrocyclic lactone abamectin primarily targets GluCl and is commonly used to control the spider mite Tetranychus urticae, an economically important crop pest. However, abamectin resistance has been reported for multiple T. urticae populations worldwide, and in several cases was associated with the mutations G314D in GluCl1 and G326E in GluCl3. Recently, an additional I321T mutation in GluCl3 was identified in several abamectin resistant T. urticae field populations. Here, we aim to functionally validate this mutation and determine its phenotypic strength.

RESULTS

The GluCl3 I321T mutation was introgressed into a T. urticae susceptible background by marker-assisted backcrossing, revealing contrasting results in phenotypic strength, ranging from almost none to 50-fold. Next, we used CRISPR-Cas9 to introduce I321T, G314D and G326E in the orthologous Drosophila GluCl. Genome modified flies expressing GluCl I321T were threefold less susceptible to abamectin, while CRISPRed GluCl G314D and G326E flies were lethal. Last, functional analysis in Xenopus oocytes revealed that the I321T mutation might reduce GluCl3 sensitivity to abamectin, but also suggested that all three T. urticae Rdls are affected by abamectin.

CONCLUSION

Three different techniques were used to characterize the role of I321T in GluCl3 in abamectin resistance and, combining all results, our analysis suggests that the I321T mutation has a complex role in abamectin resistance. Given the reported subtle effect, additional synergistic factors in resistance warrant more investigation. © 2020 Society of Chemical Industry.

Carotenoid Metabolism in Terrestrial Animals

Terrestrial animals, especially insects, contain various carotenoids that show structural diversity. These animals accumulated carotenoids derived from plants and other animals and modified them through metabolic reactions. Therefore, most of the carotenoids found in terrestrial animals originated from plants. Conversely, recent investigation revealed that some species of aphids and spider mites synthesized carotenoid themselves by carotenoid biosynthetic genes, which were horizontally transferred from fungi. In this chapter, carotenoids in terrestrial animals are described from the viewpoints of natural product chemistry, metabolism, food chain, and chemosystematics.

Carotenoid Biosynthesis in Animals: Case of Arthropods

All the organisms that belong to the animal kingdom had been believed not to synthesize carotenoids de novo. However, several groups of arthropods, which contain aphids, spider mites, and flies belonging to the family Cecidomyiidae, have been unexpectedly shown to possess carotenoid biosynthesis genes of fungal origin since 2010. On the other hand, few reports have shown direct evidence corroborating the catalytic functions of the enzymes that the carotenogenic genes encode. In the present review, we want to overview the carotenoid biosynthetic pathway of the pea aphid (Acyrthosiphon pisum), which was elucidated through functional analysis of carotenogenic genes that exist on its genome using Escherichia coli that accumulates carotenoid substrates, in addition to carotenoid biosynthesis in the other carotenogenic arthropods.

Environmental RNA interference in two-spotted spider mite, Tetranychus urticae, reveals dsRNA processing requirements for efficient RNAi response

Comprehensive understanding of pleiotropic roles of RNAi machinery highlighted the conserved chromosomal functions of RNA interference. The consequences of the evolutionary variation in the core RNAi pathway genes are mostly unknown, but may lead to the species-specific functions associated with gene silencing. The two-spotted spider mite, Tetranychus urticae, is a major polyphagous chelicerate pest capable of feeding on over 1100 plant species and developing resistance to pesticides used for its control. A well annotated genome, susceptibility to RNAi and economic importance, make T. urticae an excellent candidate for development of an RNAi protocol that enables high-throughput genetic screens and RNAi-based pest control. Here, we show that the length of the exogenous dsRNA critically determines its processivity and ability to induce RNAi in vivo. A combination of the long dsRNAs and the use of dye to trace the ingestion of dsRNA enabled the identification of genes involved in membrane transport and 26S proteasome degradation as sensitive RNAi targets. Our data demonstrate that environmental RNAi can be an efficient reverse genetics and pest control tool in T. urticae. In addition, the species-specific properties together with the variation in the components of the RNAi machinery make T. urticae a potent experimental system to study the evolution of RNAi pathways.

Biotin provisioning by horizontally transferred genes from bacteria confers animal fitness benefits

Insect symbionts are widespread in nature and lateral gene transfer is prevalent in insect symbiosis. However, the function of horizontally transferred genes (HTGs) in insect symbiosis remains speculative, including the mechanism that enables insects to feed on plant phloem deficient in B vitamins. Previously, we found there is redundancy in biotin synthesis pathways from both whitefly Bemisia tabaci and symbiotic Hamiltonella due to the presence of whitefly HTGs. Here, we demonstrate that elimination of Hamiltonella decreased biotin levels but elevated the expression of horizontally transferred biotin genes in whiteflies. HTGs proteins exhibit specific expression patterns in specialized insect cells called bacteriocytes housing symbionts. Complementation with whitefly HTGs rescued E. coli biotin gene knockout mutants. Furthermore, silencing whitefly HTGs in Hamiltonella-infected whiteflies reduced biotin levels and hindered adult survival and fecundity, which was partially rescued by biotin supplementation. Each of horizontally transferred biotin genes are conserved in various laboratory cultures and species of whiteflies with geographically diverse distributions, which shares an evolutionary origin. We provide the first experimental evidence that biotin synthesized through acquired HTGs is important in whiteflies and may be as well in other animals. Our findings suggest that B vitamin provisioning in animal-microbe symbiosis frequently evolved from bacterial symbionts to animal hosts through horizontal gene transfer events. This study will also shed light on how the animal genomes evolve through functional transfer of genes with bacterial origin in the wider contexts of microbial ecology.

Parental silencing of a horizontally transferred carotenoid desaturase gene causes a reduction of red pigment and fitness in the pea aphid

BACKGROUND

Aphids obtained carotenoid biosynthesis genes via horizontal gene transfers from fungi. However, the roles of these genes in the contributions of in aphids'adaptation and whether these genes could be used as RNAi-based pest control targets are not yet clear. Thus, in this study we used parental RNAi to analyze the potential function of a carotenoid desaturase gene (CdeB) by combined molecular and chemical approaches in the pea aphid (Acyrthosiphon pisum).

RESULTS

Transcriptional analyses showed that CdeB was significantly more highly expressed in the red morphs compared to the green ones and was associated with the production of red carotenoid. Co-transferring of pET28a-CdeB (the CdeB gene was cloned into pET28a) and pACCRT-EIB (produced lycopene) showed a deep red color in the bacterial precipitate and produced more of a red pigment, lycopene, in vitro. Parental gene-silencing of CdeB resulted in a lower body color intensity in the treated aphids and following generations in vivo. Interestingly, the dsCdeB treatment also reduced aphid performance as reflected by a delay in nymphal developmental duration, lower weight, smaller number, and altered age structure of the population.

CONCLUSION

Our results demonstrate that CdeB is involved in red color formation and the silencing of this gene by parental RNAi reduced fitness in the pea aphid. The results enhance our understanding of the biosynthesis of carotenoid in aphids and provide insights into the potential ecological significance of carotenoids in the adaptation of the aphid's biology to the environment and developing environmentally friendly control strategies for this pest.

Transcriptional changes in the aphid species Myzus cerasi under different host and environmental conditions

Aphids feature complex life cycles, which in the case of many agriculturally important species involve primary and secondary host plant species. Whilst host alternation between primary and secondary host can occur in the field depending on host availability and the environment, aphid populations maintained as laboratory stocks generally are kept under conditions that allow asexual reproduction by parthenogenesis on secondary hosts. We used Myzus cerasi (black cherry aphid) to assess aphid transcriptional differences between populations collected from primary hosts in the field and those adapted to secondary hosts under controlled environment conditions. Transfer of M. cerasi collected from local cherry trees to reported secondary host species resulted in low survival rates. Moreover, aphids were unable to survive on the secondary host land cress, unless first adapted to another secondary host, cleavers. Transcriptome analyses of the different aphid populations (field collected and adapted) revealed extensive transcriptional plasticity to a change in environment, with predominantly genes involved in redox reactions differentially regulated. Most of the differentially expressed genes were duplicated and we found evidence for differential exon usage. Our data suggest that aphid adaptation to different environments may pose a major hurdle and leads to extensive gene expression changes.

Targeted mutagenesis using CRISPR-Cas9 in the chelicerate herbivore Tetranychus urticae

The use of CRISPR-Cas9 has revolutionized functional genetic work in many organisms, including more and more insect species. However, successful gene editing or genetic transformation has not yet been reported for chelicerates, the second largest group of terrestrial animals. Within this group, some mite and tick species are economically very important for agriculture and human health, and the availability of a gene-editing tool would be a significant advancement for the field. Here, we report on the use of CRISPR-Cas9 in the spider mite Tetranychus urticae. The ovary of virgin adult females was injected with a mix of Cas9 and sgRNAs targeting the phytoene desaturase gene. Natural mutants of this laterally transferred gene have previously shown an easy-to-score albino phenotype. Albino sons of injected virgin females were mated with wild-type females, and two independent transformed lines where created and further characterized. Albinism inherited as a recessive monogenic trait. Sequencing of the complete target-gene of both lines revealed two different lesions at expected locations near the PAM site in the target-gene. Both lines did not genetically complement each other in dedicated crosses, nor when crossed to a reference albino strain with a known genetic defect in the same gene. In conclusion, two independent mutagenesis events were induced in the spider mite T. urticae using CRISPR-Cas9, hereby providing proof-of-concept that CRISPR-Cas9 can be used to create gene knockouts in mites.

Dose-Response and Temperature Dependence of the Mortality of Spider Mite and Predatory Mite Eggs Caused by Daily Nighttime Ultraviolet-B Irradiation

The two-spotted spider mite, Tetranychus urticae, is an economically important agricultural pest. A novel physical control method involving daily nighttime UV-B irradiation was recently developed for use in strawberry greenhouses. However, the overlapping of leaves after March prevents direct irradiation to T. urticae on the lower leaf surface, decreasing control effect. Excessive UV-B irradiation causes leaf sunscald in winter. Therefore, optimization of UV-B irradiance and a compensatory control agent are desired. Temperature may affect the survival of organisms exposed to UV-B, although the temperature dependence of UV-B damage is controversial. A phytoseiid mite, Neoseiulus californicus, is a prominent predator but vulnerable to a single UV-B irradiation. We compared dose-response and temperature dependence of UV-B damage between T. urticae and N. californicus eggs under daily nighttime UV-B irradiation. Unexpectedly, N. californicus showed greater resistance to UV-B than T. urticae, and the mortality was increased and decreased at low and high temperatures, respectively. This makes possible the application of UV-B doses that are lethal for spider mites but safe for phytoseiid mites. Overall, we concluded that combined use of phytoseiid mites with UV-B lamps is advantageous to spider mite management in strawberry greenhouses.

Identification and characterization of new mutations in mitochondrial cytochrome b that confer resistance to bifenazate and acequinocyl in the spider mite Tetranychus urticae

BACKGROUND

In spider mites, mutations in the mitochondrial cytochrome b Q_o pocket have been reported to confer resistance to the Q_o inhibitors bifenazate and acequinocyl. In this study, we surveyed populations of the two-spotted spider mite Tetranychus urticae for mutations in cytochrome b, linked newly discovered mutations with resistance and assessed potential pleiotropic fitness costs.

RESULTS

We identified two novel mutations in the Q_o site: G132A (equivalent to G143A in fungi resistant to strobilurins) and G126S + A133T (previously reported to cause bifenazate and acequinocyl resistance in Panonychus citri). Two T. urticae strains carrying G132A were highly resistant to bifenazate but not acequinocyl, whereas a strain with G126S + A133T displayed high levels of acequinocyl resistance, but only moderate levels of bifenazate resistance. Bifenazate and acequinocyl resistance were inherited maternally, providing strong evidence for the involvement of these mutations in the resistance phenotype. Near isogenic lines carrying G132A revealed several fitness penalties in T. urticae; a lower net reproductive rate (R₀ ), intrinsic rate of increase (rm) and finite rate of increase (LM); a higher doubling time (DT); and a more male-biased sex ratio.

CONCLUSIONS

Several lines of evidence were provided to support the causal role of newly discovered cytochrome b mutations in bifenazate and acequinocyl resistance. Because of the fitness costs associated with the G132A mutation, resistant T. urticae populations might be less competitive in a bifenazate-free environment, offering opportunities for resistance management. © 2019 Society of Chemical Industry.

Prevalence and Implications of Contamination in Public Genomic Resources: A Case Study of 43 Reference Arthropod Assemblies

Thanks to huge advances in sequencing technologies, genomic resources are increasingly being generated and shared by the scientific community. The quality of such public resources are therefore of critical importance. Errors due to contamination are particularly worrying; they are widespread, propagate across databases, and can compromise downstream analyses, especially the detection of horizontally-transferred sequences. However we still lack consistent and comprehensive assessments of contamination prevalence in public genomic data. Here we applied a standardized procedure for foreign sequence annotation to 43 published arthropod genomes from the widely used Ensembl Metazoa database. This method combines information on sequence similarity and synteny to identify contaminant and putative horizontally-transferred sequences in any genome assembly, provided that an adequate reference database is available. We uncovered considerable heterogeneity in quality among arthropod assemblies, some being devoid of contaminant sequences, whereas others included hundreds of contaminant genes. Contaminants far outnumbered horizontally-transferred genes and were a major confounder of their detection, quantification and analysis. We strongly recommend that automated standardized decontamination procedures be systematically embedded into the submission process to genomic databases.

Trait mapping in diverse arthropods by bulked segregant analysis

Bulked segregant analysis (BSA) is a cross-based method for genetic mapping in sexually reproducing organisms. The method's use of bulked (pooled) samples markedly reduces the genotyping effort associated with traditional linkage mapping studies. Further, it can be applied to species with life histories or physical attributes (as for micro-insects) that render genetic mapping with other methods impractical. Recent studies in both insects and mites have revealed that advanced BSA experimental designs can resolve causal loci to narrow genomic intervals, facilitating follow-up investigations. As high-quality genomes become more widely available, BSA methods are poised to become an increasingly important tool for the rapid mapping of both monogenic and polygenic traits in diverse arthropod species.

Oppia nitens C.L. Koch, 1836 (Acari: Oribatida): Current Status of Its Bionomics and Relevance as a Model Invertebrate in Soil Ecotoxicology

The oribatid soil mite Oppia nitens C.L. Koch, 1836, is a model microarthropod in soil ecotoxicity testing. This species has a significant role in supporting soil functions and as a suitable indicator of soil contamination. Despite its significance to the environment and to ecotoxicology, however, very little is known of its biology, ecology, and suborganismal responses to contaminants in the soil. In the present review, we present detailed and critical insights into the biology and ecology of O. nitens in relation to traits that are crucial to its adaptive responses to contaminants in soil. We used a species sensitivity distribution model to rank the species sensitivity to heavy metals (cadmium and zinc) and neonicotinoids (imidacloprid and thiacloprid) compared with other standardized soil invertebrates. Although the International Organization for Standardization and Environment and Climate Change Canada are currently standardizing a protocol for the use of O. nitens in soil toxicity testing, we believe that O. nitens is limited as a model soil invertebrate until the molecular pathways associated with its response to contaminants are better understood. These pathways can only be elucidated with information from the mites' genome or transcriptome, which is currently lacking. Despite this limitation, we propose a possible molecular pathway to metal tolerance and a putative adverse outcome pathway to heavy metal toxicity in O. nitens. Environ Toxicol Chem 2019;38:2593-2613. © 2019 SETAC.

Characterization of the Geranylgeranyl Diphosphate Synthase Gene in Acyrthosiphon pisum (Hemiptera: Aphididae) and Its Association With Carotenoid Biosynthesis

Carotenoids play many crucial roles in organisms. Recently, the de novo synthesis of carotenoids has been reported in pea aphid (Acyrthosiphon pisum) through horizontally transferred genes. However, their upstream pathway in the pea aphid is poorly understood. Geranylgeranyl diphosphate synthase (GGPPS) is the functional enzyme in the synthesis of geranylgeranyl diphosphate (GGPP) which is a precursor for the biosynthesis of many biological metabolites, including carotenoid synthesis. In this study, we performed a series of experiments to characterize GGPPS gene and its association with carotenoid biosynthesis. (1) determining the transcript abundance and carotenoid content in two geographical strain with red and green morphs, and (2) examining the abundance of carotenoid related genes and carotenoid levels after silencing of GGPPS in both red and green morphs. We observed that GGPPS was more highly expressed in the green morph than in the red morph of two strains of the pea aphid. The total level of carotenoids was also higher in green morphs than in red morphs in both strains. In addition to the total carotenoid difference, the carotenoids found in the two morphs also differed. There were α-carotene, β-carotene, and γ-carotene in the green morphs, but three additional carotenoids, including cis-torulene^∗, trans-torulene^∗, and 3,4-didehydrolycopene^∗, were present in the red morphs. Silencing the GGPPS by RNAi in both the red and green morphs decreased the expression of some carotenoid biosynthesis-related genes, including carotenoid synthase/cyclase genes and carotenoid desaturase genes in green morphs. Carotenoid levels were decreased in both green and red morphs. However, the specific carotenoids present were not changed after silencing GGPPS. These results demonstrated that GGPPS may act as the upstream enzyme to influence the synthesis of the total amount of carotenoids. The present study provided important molecular evidence for the conserved roles of GGPPS associated with carotenoids biosynthesis and will enhance further investigation on the mechanisms of carotenoid biosynthesis in pea aphid.

Carotenoids as natural functional pigments

Carotenoids are tetraterpene pigments that are distributed in photosynthetic bacteria, some species of archaea and fungi, algae, plants, and animals. About 850 naturally occurring carotenoids had been reported up until 2018. Photosynthetic bacteria, fungi, algae, and plants can synthesize carotenoids de novo. Carotenoids are essential pigments in photosynthetic organs along with chlorophylls. Carotenoids also act as photo-protectors, antioxidants, color attractants, and precursors of plant hormones in non-photosynthetic organs of plants. Animals cannot synthesize carotenoids de novo, and so those found in animals are either directly accumulated from food or partly modified through metabolic reactions. So, animal carotenoids show structural diversity. Carotenoids in animals play important roles such precursors of vitamin A, photo-protectors, antioxidants, enhancers of immunity, and contributors to reproduction. In the present review, I describe the structural diversity, function, biosyntheses, and metabolism of natural carotenoids.

Convergent evolution of cytochrome P450s underlies independent origins of keto-carotenoid pigmentation in animals

Keto-carotenoids contribute to many important traits in animals, including vision and coloration. In a great number of animal species, keto-carotenoids are endogenously produced from carotenoids by carotenoid ketolases. Despite the ubiquity and functional importance of keto-carotenoids in animals, the underlying genetic architectures of their production have remained enigmatic. The body and eye colorations of spider mites (Arthropoda: Chelicerata) are determined by β-carotene and keto-carotenoid derivatives. Here, we focus on a carotenoid pigment mutant of the spider mite Tetranychus kanzawai that, as shown by chromatography, lost the ability to produce keto-carotenoids. We employed bulked segregant analysis and linked the causal locus to a single narrow genomic interval. The causal mutation was fine-mapped to a minimal candidate region that held only one complete gene, the cytochrome P450 monooxygenase CYP384A1, of the CYP3 clan. Using a number of genomic approaches, we revealed that an inactivating deletion in the fourth exon of CYP384A1 caused the aberrant pigmentation. Phylogenetic analysis indicated that CYP384A1 is orthologous across mite species of the ancient Trombidiformes order where carotenoids typify eye and body coloration, suggesting a deeply conserved function of CYP384A1 as a carotenoid ketolase. Previously, CYP2J19, a cytochrome P450 of the CYP2 clan, has been identified as a carotenoid ketolase in birds and turtles. Our study shows that selection for endogenous production of keto-carotenoids led to convergent evolution, whereby cytochrome P450s were independently co-opted in vertebrate and invertebrate animal lineages.

High-resolution QTL mapping in Tetranychus urticae reveals acaricide-specific responses and common target-site resistance after selection by different METI-I acaricides

Arthropod herbivores cause dramatic crop losses, and frequent pesticide use has led to widespread resistance in numerous species. One such species, the two-spotted spider mite, Tetranychus urticae, is an extreme generalist herbivore and a major worldwide crop pest with a history of rapidly developing resistance to acaricides. Mitochondrial Electron Transport Inhibitors of complex I (METI-Is) have been used extensively in the last 25 years to control T. urticae around the globe, and widespread resistance to each has been documented. METI-I resistance mechanisms in T. urticae are likely complex, as increased metabolism by cytochrome P450 monooxygenases as well as a target-site mutation have been linked with resistance. To identify loci underlying resistance to the METI-I acaricides fenpyroximate, pyridaben and tebufenpyrad without prior hypotheses, we crossed a highly METI-I-resistant strain of T. urticae to a susceptible one, propagated many replicated populations over multiple generations with and without selection by each compound, and performed bulked segregant analysis genetic mapping. Our results showed that while the known H92R target-site mutation was associated with resistance to each compound, a genomic region that included cytochrome P450-reductase (CPR) was associated with resistance to pyridaben and tebufenpyrad. Within CPR, a single nonsynonymous variant distinguished the resistant strain from the sensitive one. Furthermore, a genomic region linked with tebufenpyrad resistance harbored a non-canonical member of the nuclear hormone receptor 96 (NHR96) gene family. This NHR96 gene does not encode a DNA-binding domain (DBD), an uncommon feature in arthropods, and belongs to an expanded family of 47 NHR96 proteins lacking DBDs in T. urticae. Our findings suggest that although cross-resistance to METI-Is involves known detoxification pathways, structural differences in METI-I acaricides have also resulted in resistance mechanisms that are compound-specific.