Phylogeny of the spider mite sub-family Tetranychinae (Acari: Tetranychidae) inferred from RNA-Seq data

Phylogenomics offers new insights into the classification of Phytoseiidae (Acari: Mesostigmata)

Phytoseiid mites are significant natural predators of harmful mites and constitute one of the largest groups within Gamasina (Acari: Mesostigmata). The currently accepted classification divides the Phytoseiidae family into three subfamilies, primarily based on the pattern of their dorsal setae. However, the phylogenetic relationships among these subfamilies remain unresolved. To address this issue, we sampled forty representative species from the three subfamilies. Using a specific Arachnida reference dataset (orthodb10, n = 2,934), we mined thousands of universal single-copy orthologs from whole-genome sequencing data. We then constructed four amino-acid matrices, taking into account evolutionary rates and the degree of violation of the molecular clock (DVMC). Phylogenetic trees were reconstructed using both concatenated and multispecies coalescent (MSC) analyses. Based on maximum likelihood and Bayesian inference, the majority of the phylogenetic trees supported the hypothesis (P2) of Phytoseiinae + (Typhlodrominae + (Galendromus + Amblyseiinae)). However, when using slowly evolving and non-clock-like genes, the MSC trees supported an alternative hypothesis (P1) of Typhlodrominae + (Phytoseiinae + (Galendromus + Amblyseiinae)). Additional analyses, including model fitness, topology tests, and morphological comparisons, favored the hypothesis P2. Our findings indicate that Typhlodrominae is not monophyletic, and Galendromus and Amblyseiinae are sister groups. Based on these results, we recommend that Galendromus be separated from Typhlodrominae and elevated to a fourth subfamily.

Study on the variations in acaricide sensitivity between two spider mite species, Amphitetranychus viennensis and Tetranychus urticae, in Chinese orchards

Amphitetranychus viennensis and Tetranychus urticae, are destructive agricultural and horticultural pests. Their management primarily relies on acaricides; however, little is known about the susceptibility of these two species to these chemicals. The current study assessed the susceptibility of A. viennensis and T. urticae to ten acaricides, investigated the detoxification enzyme activities, and conducted transcriptional analyses after bifenazate and cyetpyrafen exposure. The results showed that the LC50 values of most acaricides against T. urticae were notably higher than those for A. viennensis at different developmental stages. At the adult stage, A. viennensis was more tolerant to bifenazate than T. urticae, while A. viennensis showed increased sensitivity to cyetpyrafen than T. urticae. After cyetpyrafen exposure, glutathione S-transferases (GSTs) activity in T. urticae were markedly higher at 6 and 12 h, whereas that in A. viennensis increased only at 6 h. No notable differences in cytochrome P450 monooxygenases (P450s) levels were found in T. urticae between the control and treatment groups (cyetpyrafen or bifenazate). However, A. viennensis treated with either cyetpyrafen or bifenazate showed a marked decrease in P450 levels at 12 h. Furthermore, more detoxification genes in both species were activated in response to bifenazate or cyetpyrafen. Differential metabolic detoxification mediated by P450 and GST genes may primarily account for the distinct responses of these species to bifenazate and cyetpyrafen. These findings reveal the distinct detoxification capacities of the two species in response to acaricides and highlight the importance of applying species-specific management strategies for these pests.

Wolbachia strengthens the match between premating and early postmating isolation in spider mites

Endosymbiotic reproductive manipulators are widely studied as sources of postzygotic isolation in arthropods, but their effect on prezygotic isolation between genetically differentiated populations has garnered less attention. We tested this using two partially isolated populations of the red and green color forms of Tetranychus urticae, either uninfected or infected with different Wolbachia strains, one inducing cytoplasmic incompatibility and the other not. We first investigated male and female preferences and found that, in absence of infection, females were not choosy, but all males preferred red-form females. Wolbachia effects were more subtle, with only the cytoplasmic incompatibility-inducing strain slightly strengthening color-form-based preferences. We then performed a double-mating experiment to test how incompatible matings affect subsequent mating behavior and offspring production as compared to compatible matings. Females mated with an incompatible male (infected and/or heterotypic) were more attractive and/or receptive to subsequent (compatible) matings, although analyses of offspring production revealed no clear benefit for this remating behavior (i.e., apparently unaltered first male sperm precedence). Finally, by computing the relative contributions of each reproductive barrier to total isolation, we showed that premating isolation matches both host-associated and Wolbachia-induced postmating isolation, suggesting that Wolbachia could contribute to reproductive isolation in this system.

Decoding plant-induced transcriptomic variability and consistency in two related polyphagous mites differing in host ranges

The diet breadth of generalist herbivores when compared to specialists tends to be associated with greater transcriptional plasticity. Here, we consider whether it may also contribute to variation in host range among two generalists with different levels of polyphagy. We examined two related polyphagous spider mites with different host ranges, Tetranychus urticae (1200 plants) and Tetranychus truncatus (90 plants). Data from multiple populations of both species domesticated on common beans and transferred to new plant hosts (cotton, cucumber, eggplant) were used to investigate transcriptional plasticity relative to population-based variation in gene expression. Compared to T. truncatus, T. urticae exhibited much higher transcriptional plasticity. Populations of this species also showed much more variable expression regulation in response to a plant host, particularly for genes related to detoxification, transport, and transcriptional factors. In response to the different plant hosts, both polyphagous species showed enriched processes of drug/xenobiotics metabolism, with T. urticae orchestrating a relatively broader array of biological pathways. Through co-expression network analysis, we identified gene modules associated with host plant response, revealing shared hub genes primarily involved in detoxification metabolism when both mites fed on the same plants. After silencing a shared hub CYP gene related to eggplant exposure, the performance of both species on the original bean host improved, but the fecundity of T. truncatus decreased when feeding on eggplant. The extensive transcriptomic variation shown by T. urticae might serve as a potential compensatory mechanism for a deficiency of hub genes in this species. This research points to nuanced differences in transcriptomic variability between generalist herbivores.

The development of an egg-soaking method for delivering dsRNAs into spider mites

Recently, the first sprayable RNAi biopesticide, Ledprona, against the Colorado potato beetle, Leptinotarsa decemlineata, has been registered at the United States Environmental Protection Agency. Spider mites (Acari: Tetranychidae), a group of destructive agricultural and horticultural pests, are notorious for rapid development of insecticide/acaricide resistance. The management options, on the other hand, are extremely limited. RNAi-based biopesticides offer a promising control alternative to address this emerging issue. In this study, we i) developed an egg-soaking dsRNA delivery method; ii) evaluated the factors influencing RNAi efficiency, and finally iii) investigated the potential mode of entry of this newly developed egg-soaking RNAi method. In comparison to other dsRNA delivery methods, egg-soaking method was the most efficient, convenient/practical, and cost-effective method for delivering dsRNAs into spider mites. RNAi efficiency of this RNAi method was affected by target genes, dsRNA concentration, developmental stages, and mite species. In general, the hawthorn spider mite, Amphitetranychus viennensis, is more sensitive to RNAi than the two-spotted spider mite, Tetranychus urticae, and both of them have dose-dependent RNAi effect. For different life stages, egg and larvae are the most sensitive life stages to dsRNAs. For different target genes, there is no apparent association between the suppression level and the resultant phenotype. Finally, we demonstrated that this egg-soaking RNAi method acts as both stomach and contact toxicity. Our combined results demonstrate the effectiveness of a topically applied dsRNA delivery method, and the potential of a spray induced gene silencing (SIGS) method as a control alternative for spider mites.

A chromosome-level genome assembly of the spider mite Tetranychus piercei McGregor

Despite the rapid advances in sequencing technology, limited genomic resources are currently available for phytophagous spider mites, which include many important agricultural pests. One of these pests is Tetranychus piercei (McGregor), a serious banana pest in East Asia exhibiting remarkable tolerance to high temperature. In this study, we assembled a high-quality genome of T. piercei using a combination of PacBio long reads and Illumina short reads sequencing. With the assistance of chromatin conformation capture technology, 99.9% of the contigs were anchored into three pseudochromosomes with a total size of 86.02 Mb. Repetitive elements, accounting for 14.16% of this genome (12.20 Mb), are predominantly composed of long-terminal repeats (30.7%). By combining evidence of ab initio prediction, transcripts, and homologous proteins, we annotated 11,881 protein-coding genes. Both the genome and proteins have high BUSCO completeness scores (>94%). This high-quality genome, along with reliable annotation, provides a valuable resource for investigating the high-temperature tolerance of this species and exploring the genomic basis that underlies the host range evolution of spider mites.

Hybridisation between host races broadens the host range of offspring in Eotetranychus asiaticus (Acari: Tetranychidae)

Host adaptation in herbivorous arthropods is one of the first steps to sympatric speciation, and spider mites (Acari: Tetranychidae) are useful model organisms for studying this phenomenon. Many researchers have studied the process of host adaptation via artificial selection experiments. Recent analyses suggest that hybridisation has diversified host ranges, although empirical evidence is scarce. We explored the host exploitation of two strains of Eotetranychus asiaticus established from Ternstroemia gymnanthera (Pentaphylacaceae) and Japanese cinnamon, Cinnamomum yabunikkei (Lauraceae), and evaluated the effect of hybridisation on offspring host use. Transplant experiments showed that females oviposited and immature mites developed only on their native hosts, suggesting specialisation to the secondary metabolites of each host plant. However, F1 hybrids from reciprocal crosses developed on both host plants (survival rate: 92-100%) with normal female-biased sex ratios. Furthermore, all backcrosses to the parental strains yielded B1 offspring that were also viable on both host plants with normal sex ratios (69-87% and 39-92% females on T. gymnanthera and C. yabunikkei, respectively). B1 survival rates in interstrain crosses were varied (11-63%) and lower than those in intrastrain crosses (88-93%). We could not detect any reproductive barriers in these experiments, and host preference may be the sole factor determining pre-mating isolation. The survival rates and sex ratios we observed suggest cytochromosome interactions. In conclusion, hybridisation, which results in heterozygotes and recombination, is an underexplored way to provide spider mites with a novel host plant.

Molecular-Based Taxonomic Inferences of Some Spider Mite Species of the Genus Oligonychus Berlese (Acari, Prostigmata, Tetranychidae)

DNA barcoding technology using short DNA sequences has emerged as an efficient and reliable tool for identifying, confirming, and resolving closely related taxa. This study used ITS2-rDNA and mtCOI DNA sequences to confirm the identity of eight Oligonychus species, representing 68 spider mite samples, collected mainly from Saudi Arabia (SA) and some from Mexico, Pakistan, USA, and Yemen. The intraspecific nucleotide divergences of the studied Oligonychus species ranged from 0% to 1.2% for ITS2 and 0% to 2.9% for COI. However, the interspecific nucleotide divergences were distinctly higher than the intraspecific ones and ranged from 3.7% to 51.1% for ITS2 and 3.2% to 18.1% for COI. Furthermore, molecular data correctly confirmed the species identity of 42 Oligonychus samples lacking males, including a previously claimed sample of O. pratensis from SA. High genetic variations were detected in two Oligonychus species: O. afrasiaticus (McGregor) (nine ITS2 and three COI haplotypes) and O. tylus Baker and Pritchard (four ITS2 and two COI haplotypes). In addition, ITS2- and COI-based phylogenetic trees confirmed the subdivision of the genus Oligonychus. In conclusion, integrative taxonomic approaches are vital to resolve the closely related Oligonychus species, identify the samples lacking male specimens, and assess phylogenetic relationships within and among species.

Phylogenetic-Related Divergence in Perceiving Suitable Host Plants among Five Spider Mites Species (Acari: Tetranychidae)

Spider mites belonging to the genus Tetranychus infest many important agricultural crops in both fields and greenhouses worldwide and are diversified in their host plant range. How spider mites perceive their suitable host plants remains not completely clear. Here, through two-host-choice designs (bean vs. tomato, and bean vs. eggplant), we tested the efficacies of the olfactory and gustatory systems of five spider mite species (T. urticae, T. truncatus, T. pueraricola, T. piercei, and T. evansi), which differ in host plant range in sensing their suitable host plant, by Y-tube olfactometer and two-choice disc experiments. We found that spider mites cannot locate their suitable host plants by volatile odours from a long distance, but they can use olfactory sensation in combination with gustatory sensation to select suitable host plants at a short distance. Highly polyphagous species displayed strong sensitivity in sensing suitable host plants rather than the lowered sensitivity we expected. Intriguingly, our principal component analyses (PCAs) showed that the similarity among five spider mite species in the performance of perceiving suitable host plants was highly correlated with their relative phylogenetic relationships, suggesting a close relationship between the chemosensing system and the speciation of spider mites. Our results highlight the necessity of further work on the chemosensing system in relation to host plant range and speciation of spider mites.

Molecular identification and phylogenetic analysis of spider mites (Prostigmata: Tetranychidae) of Turkey

The family Tetranychidae includes many agriculturally important species known as spider mites. Their morphological identification is quite difficult due to the tiny size of their taxonomic characters and the requirement for high-level expertise. This may lead to pest misidentification and thus failure in pest management. DNA-based species identification seems to offer an alternative solution to overcome these issues. In the present study, two common molecular markers-Cytochrome oxidase subunit I (COI) and Internal transcribed spacer 2 (ITS2)-were used to identify 10 spider mite species from Turkey. Furthermore, genetic distances for several of them were assessed. Panonychus ulmi and Bryobia kissophila had the lowest (1.1%) and highest (4.5%) intra-specific genetic distances, respectively. In addition, integrative taxonomy allowed to identify Eotetranychus quercicola in Turkey as a new record. The sequences herein obtained will allow rapid species identification using molecular techniques and will contribute to resolve the phylogenetic history of spider mites.

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.

Wolbachia and host intrinsic reproductive barriers contribute additively to postmating isolation in spider mites

Wolbachia are maternally-inherited bacteria that induce cytoplasmic incompatibility in many arthropod species. However, the ubiquity of this isolation mechanism for host speciation processes remains elusive, as only few studies have examined Wolbachia-induced incompatibilities when host populations are not genetically compatible. Here, we used three populations of two genetically differentiated colour forms of the haplodiploid spider mite Tetranychus urticae to dissect the interaction between Wolbachia-induced and host-associated incompatibilities, and their relative contribution to postmating isolation. We found that these two sources of incompatibility act through different mechanisms in an additive fashion. Host-associated incompatibility contributes 1.5 times more than Wolbachia-induced incompatibility in reducing hybrid production, the former through an overproduction of haploid sons at the expense of diploid daughters (ca. 75% decrease) and the latter by increasing the embryonic mortality of daughters (by ca. 49%). Furthermore, regardless of cross direction, we observed near-complete F1 hybrid sterility and complete F2 hybrid breakdown between populations of the two forms, but Wolbachia did not contribute to this outcome. We thus show mechanistic independence and an additive nature of host-intrinsic and Wolbachia-induced sources of isolation. Wolbachia may contribute to reproductive isolation in this system, thereby potentially affecting host differentiation and distribution in the field.

Photoperiodic control of reproductive arrest in the oak-inhabiting spider mite Schizotetranychus brevisetosus (Acari: Tetranychidae)

Populations of Schizotetranychus brevisetosus Ehara (Acari: Tetranychidae), which live on the evergreen oak (Quercus glauca), survive the coldest months as either adult females or winter eggs. Adult females comprise the majority of the population in early November and oviposit from late November to early March. Most winter eggs hatch by late March, and adults of the next generation emerge in April. This species is considered an egg-diapausing species, but the environmental cues that regulate female reproductive arrest and resumption are mostly unknown. We investigated the photoperiodic responses of autumn reproductive arrest in 10 populations collected from different elevations in Shikoku, Japan. All populations showed long-day responses to critical daylength (CDL) around 12.2 h light (12.2L) at 20 °C, though there was no linear relationship between CDL and altitude. This result explains the steep decline in the proportion of summer eggs in November. Nonreproductive females developed under 10L at 20 °C commenced oviposition 14.3-20.6 days after transferring to 15L. This long pre-oviposition period explains the reduction in eggs before winter reproduction and suggests shallow adult diapause. Eggs thus obtained hatched in 12.9-15.3 days, similarly to summer eggs. Therefore, egg diapause in S. brevisetosus is much shallower than in species on deciduous hosts, which lay their winter eggs in early autumn to hatch at leaf flush in spring. The reproductive arrest and short hatching period may be an adaptation allowing egg-laying in midwinter, when predation pressure is low.

Tracing foreign sequences in plant transcriptomes and genomes using OCT4, a POU domain protein

Contaminations in sequencing data, especially in reference genomes, lead to inevitable errors in downstream analyses. Similarly, presence of contaminants in transcriptomes, misrepresents the molecular basis of various interactions. In this study, we report the presence of a large number of plant transcriptomes contaminated with RNAs encoding POU domain proteins; a family of proteins that has not been reported in plants and fungi. Besides, our findings illustrated that there are four POU domain protein-coding sequences in the reference genome of Rhodamnia argentea. It turned out that the existing foreign fragments are related to arthropods that are considered as plant pests. We also identified two contaminated draft genomes, Humulus lupulus and Cannabis sativa that contained complete rDNA sequences originating from Tetranychus species. As a result, careful screening of sequencing data before releasing them in public databases or checking existing genomes for possible contaminations is recommended.

Production of winter eggs in Schizotetranychus brevisetosus (Acari: Tetranychidae) inhabiting evergreen Japanese blue oak

The overwintering pattern of parasitic herbivorous arthropods is closely related to host phenology, because defoliation imposes strong selection pressures on various developmental stages. This relationship has been well studied in populations of spider mites (Acari: Tetranychidae) on deciduous hosts, but is little studied in populations on evergreen hosts, probably because their leaves are always available. However, spring defoliation may also influence the life cycle. We studied the overwintering pattern of Schizotetranychus brevisetosus (Acari: Tetranychidae), a specialist on evergreen oak, Quercus glauca, in Kochi, Japan. Only adult females and their eggs (winter eggs) survived the coldest months. We also observed a conspicuous seasonal change in egg colour and size: December winter eggs were 1.7× larger than September summer eggs, suggesting the winter eggs are diapausing. Adult females produced summer eggs until November and winter eggs from late November until they disappeared in March. The winter eggs hatched in early March. The immature stages developed in mid- to late March, when 39% of old leaves fell, some of which carried hundreds of immature individuals. Therefore, even in evergreen hosts, defoliation places potentially strong selection pressure on the immature stages. Despite this, S. brevisetosus appears not to change its egg hatching season to avoid the defoliation season, so it may have evolved a behavioural adaptation to escape falling leaves. The existence of several species with similar lifestyles suggests the importance of host phenology and predation pressure for evolution of the overwintering pattern.

High genetic diversity in a 'recent outbreak' spider mite, Tetranychus pueraricola, in mainland China

Tetranychus pueraricola is a newly reported spider mite that occurs frequently in mainland China. It is possible that this species was introduced from elsewhere and became a serious pest recently. However, the correct identification of red-pigmented spider mites has repeatedly proven problematic. There is also the possibility that T. pueraricola in China was long misidentified as its sibling species, Tetranychus urticae (red form). To test which of these two scenarios is the more likely, individuals from 14 populations of T. pueraricola and five populations of T. urticae (red form) in China were sampled and genotyped using mitochondrial COI and microsatellite loci. Unlike a recent invasive species, the genetic diversity of T. pueraricola was very high with high mitochondrial genetic diversity (16 haplotypes), high effective alleles (Ne = 2.038 ± 0.081) and expected heterozygosity (He = 0.395 ± 0.016). Surprisingly, we found that all T. urticae (red form) populations shared only one mitochondrial haplotype and showed quite low genetic diversity (Ne = 1.443 ± 0.055; He = 0.234 ± 0.025) which was even lower than that of the green form of T. urticae in mainland China from a previous study. We did not detect significant signals of recent bottlenecks for most populations from both species. These results suggest T. pueraricola is unlikely to be a recent invasive pest but a species that has existed in China for a long time. It is probable that T. pueraricola in China has long been misidentified as T. urticae (red form).

A New Prevalent Densovirus Discovered in Acari. Insight from Metagenomics in Viral Communities Associated with Two-Spotted Mite (Tetranychus urticae) Populations

Viral metagenomics and high throughput sequence mining have revealed unexpected diversity, and the potential presence, of parvoviruses in animals from all phyla. Among arthropods, this diversity highlights the poor knowledge that we have regarding the evolutionary history of densoviruses. The aim of this study was to explore densovirus diversity in a small arthropod pest belonging to Acari, the two-spotted spider mite Tetranychus urticae, while using viral metagenomics based on virus-enrichment. Here, we present the viromes obtained from T. urticae laboratory populations made of contigs that are attributed to nine new potential viral species, including the complete sequence of a novel densovirus. The genome of this densovirus has an ambisens genomic organization and an unusually compact size with particularly small non-structural proteins and a predicted major capsid protein that lacks the typical PLA2 motif that is common to all ambidensoviruses described so far. In addition, we showed that this new densovirus had a wide prevalence across populations of mite species tested and a genomic diversity that likely correlates with the host phylogeny. In particular, we observed a low densovirus genomic diversity between the laboratory and natural populations, which suggests that virus within-species evolution is probably slower than initially thought. Lastly, we showed that this novel densovirus can be inoculated to the host plant following feeding by infected mites, and circulate through the plant vascular system. These findings offer new insights into densovirus prevalence, evolution, and ecology.