Genomic insights into mite phylogeny, fitness, development, and reproduction

Exploring the role of FBXL fbxl gene family in Soybean: Implications for plant height and seed size regulation

F-box proteins constitute a significant family in eukaryotes and, as a component of the Skp1p-cullin-F-box complex, are considered critical for cellular protein degradation and other biological processes in plants. Despite their importance, the functions of F-box proteins, particularly those with C-terminal leucine-rich repeat (LRR) domains, remain largely unknown in plants. Therefore, the present study conducted genome-wide identification and in silico characterization of F-BOX proteins with C-terminal LRR domains in soybean (Glycine max L.) (GmFBXLs). A total of 45 GmFBXLs were identified. The phylogenetic analysis showed that GmFBXLs could be subdivided into ten subgroups and exhibited a close relationship with those from Arabidopsis thaliana, Cicer aretineum, and Medicago trunculata. It was observed that most cis-regulatory elements in the promoter regions of GmFBXLs are involved in hormone signalling, stress responses, and developmental stages. In silico transcriptome data illustrated diverse expression patterns of the identified GmFBXLs across various tissues, such as shoot apical meristem, flower, green pods, leaves, nodules, and roots. Overexpressing (OE) GmFBXL12 in Tianlong No.1 cultivar resulted in a significant difference in seed size, number of pods, and number of seeds per plant, indicated a potential increase in yield compared to wild type. This study offers valuable perspectives into the role of FBXLs in soybean, serving as a foundation for future research. Additionally, the identified OE lines represent valuable genetic resources for enhancing seed-related traits in soybean.

Diversity and Distribution of Mites (ACARI) Revealed by Contamination Survey in Public Genomic Databases

Acari (mites and ticks) are a biodiverse group of microarthropods within the Arachnida. Because of their diminutive size, mites are often overlooked. We hypothesized that mites, like other closely related microorganisms, could also contaminate public genomic database. Here, using a strategy based on DNA barcodes previously reported, we scanned contaminations related to mites (Acari, exclusive of Ixodida) in Genbank WGS/TSA database. In 22,114 assemblies (17,845 animal and 4269 plant projects), 1717 contigs in 681 assemblies (3.1%) were detected as mite contaminations. Additional taxonomic analysis showed the following: (1) most of the contaminants (1445/1717) were from the specimens of Magnoliopsida, Insecta and Pinopsida; (2) the contamination rates were higher in plant or TSA projects; (3) mite distribution among different classes of hosts varied considerably. Additional phylogenetic analysis of these contaminated contigs further revealed complicated mite-host associations. Overall, we conducted a first systemic survey and analysis of mite contaminations in public genomic database, and these DNA barcode related mite contigs will provide a valuable resource of information for understanding the diversity and phylogeny of mites.

Expression and functional characterization of odorant-binding protein 2 in the predatory mite Neoseiulus barkeri

Olfaction plays a crucial role for arthropods in foraging, mating, and oviposition. The odorant-binding protein (OBP) gene is considered one of the most important olfactory genes. However, little is known about its functions in predatory mites. Here, we used Neoseiulus barkeri, an important commercialized natural pest control, to explore the chemosensory characteristics of OBP. In this study, N. barkeri was attracted by methyl salicylate (MeSA) and showed higher crawling speeds under MeSA treatment. Then, we identified and cloned an OBP gene named Nbarobp2 and analyzed its expression profiles in the predatory mite. Nbarobp2 was 663 bp, was highly expressed in larval and nymphal stages, and was significantly upregulated in N. barkeri under MeSA treatment. Nbarobp2 encoded 202 amino acid residues with a molecular weight of 23 kDa (after removing the signal peptide). Sequence comparisons revealed that the OBPs in Arachnida shared 6 conserved cysteine sites, but were distinguishable from the OBPs of Insecta on the phylogenetic tree. RNA interference, Western blotting, and binding affinity assays further proved that Nbarobp2 was involved in volatile perception in predatory mites. This study shed light on the functional characteristics of OBPs in predatory mites, providing a new insight for better biological control.

The Impact of Whole Genome Duplication on the Evolution of the Arachnids

The proliferation of genomic resources for Chelicerata in the past 10 years has revealed that the evolution of chelicerate genomes is more dynamic than previously thought, with multiple waves of ancient whole genome duplications affecting separate lineages. Such duplication events are fascinating from the perspective of evolutionary history because the burst of new gene copies associated with genome duplications facilitates the acquisition of new gene functions (neofunctionalization), which may in turn lead to morphological novelties and spur net diversification. While neofunctionalization has been invoked in several contexts with respect to the success and diversity of spiders, the overall impact of whole genome duplications on chelicerate evolution and development remains imperfectly understood. The purpose of this review is to examine critically the role of whole genome duplication on the diversification of the extant arachnid orders, as well as assess functional datasets for evidence of subfunctionalization or neofunctionalization in chelicerates. This examination focuses on functional data from two focal model taxa: the spider Parasteatoda tepidariorum, which exhibits evidence for an ancient duplication, and the harvestman Phalangium opilio, which exhibits an unduplicated genome. I show that there is no evidence that taxa with genome duplications are more successful than taxa with unduplicated genomes. I contend that evidence for sub- or neofunctionalization of duplicated developmental patterning genes in spiders is indirect or fragmentary at present, despite the appeal of this postulate for explaining the success of groups like spiders. Available expression data suggest that the condition of duplicated Hox modules may have played a role in promoting body plan disparity in the posterior tagma of some orders, such as spiders and scorpions, but functional data substantiating this postulate are critically missing. Spatiotemporal dynamics of duplicated transcription factors in spiders may represent cases of developmental system drift, rather than neofunctionalization. Developmental system drift may represent an important, but overlooked, null hypothesis for studies of paralogs in chelicerate developmental biology. To distinguish between subfunctionalization, neofunctionalization, and developmental system drift, concomitant establishment of comparative functional datasets from taxa exhibiting the genome duplication, as well as those that lack the paralogy, is sorely needed.

A review of the molecular mechanisms of acaricide resistance in mites and ticks

The Arachnida subclass of Acari comprises many harmful pests that threaten agriculture as well as animal health, including herbivorous spider mites, the bee parasite Varroa, the poultry mite Dermanyssus and several species of ticks. Especially in agriculture, acaricides are often used intensively to minimize the damage they inflict, promoting the development of resistance. Beneficial predatory mites used in biological control are also subjected to acaricide selection in the field. The development and use of new genetic and genomic tools such as genome and transcriptome sequencing, bulked segregant analysis (QTL mapping), and reverse genetics via RNAi or CRISPR/Cas9, have greatly increased our understanding of the molecular genetic mechanisms of resistance in Acari, especially in the spider mite Tetranychus urticae which emerged as a model species. These new techniques allowed to uncover and validate new resistance mutations in a larger range of species. In addition, they provided an impetus to start elucidating more challenging questions on mechanisms of gene regulation of detoxification associated with resistance.

Negative Impact of Unstable Spiromesifen Resistance on Fitness of Tetranychus urticae (Acari: Tetranychidae)

Two-spotted spider mite, Tetranychus urticae Koch (Acari: Tetranychidae), is a phytophagous haplodiploid mite and its control is largely based on the use of pesticides. But, the short life cycle and high reproductive rate allow them to develop resistance to many pesticides. To design a strategy for resistance management, a fitness cost study was conducted on different populations of T. urticae, i.e., spiromesifen selected (SPIRO-SEL), unselected (Unsel), and reciprocal crosses. After twelve rounds of selections, T. urticae developed high spiromesifen resistance (71.7-fold) compared to the Unsel strain. Results showed a fitness cost for SPIRO-SEL, Cross1 (Unsel ♀ × SPIRO-SEL ♂), and Cross2 (SPIRO-SEL ♀ × Unsel ♂) with a relative fitness values of 0.63, 0.86, and 0.70, respectively. There was a significant increase in the incubation period, quiescent larvae, and egg to adult male and female developmental period of the SPIRO-SEL compared with Unsel strain. Moreover, resistance to spiromesifen was unstable with a decline in resistance value of - 0.05. The presence of unstable spiromesifen resistance associated with fitness costs suggests that intermittent withdrawal of its usage could potentially preserve its effectiveness for management of T. urticae.

Do mites eat and run? A systematic review of feeding and dispersal strategies

Dispersal is an important process affecting the survival of organisms and the structure and dynamics of communities and ecosystems in space and time. It is a multiphase phenomenon influenced by many internal and external factors. Dispersal syndromes can be complicated, but they are vital to our knowledge of the biology of any organism. We analysed dispersal ability in mites (Acariformes and Parasitiformes), a highly diverse group of wingless arthropods, taking into consideration various modes of dispersal, feeding strategies, body size and the number of articles published for each species. Based on 174 articles summarized for this study, it appears that mites are opportunistic when it comes to dispersal, regardless of their feeding habits, and are often able to adopt several different strategies as needs arise. Moreover, we find a significant positive relationship between the amount of research effort that was put into studying a given species and the number of modes of dispersal that were described. The most salient conclusion to be drawn from this positive correlation is that additional studies are needed, especially on a broader set of mite taxa, until the aforementioned correlation is no longer demonstrably significant.

Expression and functional analysis of Niemann-Pick C2 gene in Phytoseiulus persimilis

As a new protein class of semiochemical binding and transporting, Niemann-Pick proteins type C2 (NPC2) in arthropods have received more attentions in recent decade. However, the gene function has not been studied in phytoseiid mites with biocontrol potential. In the current study, we cloned a NPC2 gene PpNPC2a from the transcriptome of Phytoseiulus persimilis Athias-Henriot. By encoding 181 amino acids with a conserved ML domain, PpNPC2a was found a homolog of NPC2-1 in Galendromus occidentalis Nesbitt. We then measured the spatio-temporal expression of PpNPC2a in P. persimilis, and found the highest expression in female adults compared to other stages. Due to the tiny body size of predatory mites, we only examined tissue expressions in two sections: the anterior part (gnathosoma and the first pair of legs) and the posterior part (idiosoma without the first pair of legs). Higher transcription of PpNPC2a was found in the posterior part. To investigate the potential function of PpNPC2a in P. persimilis, we interfered gene expression in female adults by feeding dsRNA, which resulted in a decrease of relative expression by 59.1 and 78.2% after 24 and 72 h, respectively. Compared with the control, dsNPC2a-treated P. persimilis were insensitive to the scent of leaves or plants infested by spider mites, suggesting a role of PpNPC2a in response to plant volatiles. However, the dsNPC2a-interfered mites could still respond to four representative compounds of herbivore-induced plant volatiles, including 4,8,12-trimethyl-1,3,7,11-tridecatetraene (TMTT), methyl salicylate (MeSA), β-caryophyllene and linalool. In short, our results indicated PpNPC2a may be involved in the chemosensory process of P. persimilis in response to whole-plant volatiles.

Assembly of a Draft Genome for the Mouse Ectoparasite Myocoptes musculinus

Myocoptes musculinus is a common ectoparasite of wild mice and is occasionally found on research mice. Infestations of research mice are often subclinical but can cause severe dermatitis. Perhaps more importantly, infestations can cause immunologic reactions that may alter research outcomes, and most animal research facilities strive to prevent or eliminate mites from their mouse colonies. M. musculinus infestations are currently detected by using microscopic evaluation of the fur and skin and PCR assays of pelt swabs targeting the rRNA genes of this mite. In our facility, we encountered multiple, false-positive 18S rRNA PCR results from a closed mouse colony. We could not identify the source of the false positives even after performing PCR analysis of other Myocoptes gene targets using assays developed from the few other target genomic sequences available for M. musculinus or Myocoptes japonensis in public databases. This situation highlighted the limited genetic resources available for development of diagnostic tests specific for this ectoparasite. To expand the available genetic resources, we generated a metagenome of M. musculinus derived by sequencing from fur plucks of an infected mouse. We also determined the completeness of this metagenome and compared it with those of related mites.

Identification of potential sex determination genes and functional analyses in Neoseiulus californicus under prey stress

BACKGROUND

Phytoseiid mites are important natural enemies of spider mites. Sex-determination mechanism are important basic scientific issues in the reproduction and evolution of predatory mites. Clarifying sex-determination mechanism may provide reference for exploring genetic approach to have the phytoseiid mites produce more female offspring, which could improve their effectiveness as a biological control agent.

RESULTS

We used transcriptome sequencing to identify and characterize 20 putative sex-determination genes in the phytoseiid mite Neoseiulus californicus, a species with uncommon pseudo-arrhenotoky, including doublesex-like (dsx1-like), transformer-2 (tra-2), intersex (ix), and fruitless-like (BTB2). A significant negative correlation was found between prey stress and offspring sex ratio. But the most genes identified showed no difference in expression between the groups with lowest and highest female offspring ratios. The hatching rate and sex ratio of female offspring were reduced when the ix gene was silenced, and the oviposition days and fecundity were reduced when the BTB2 gene was silenced. The fecundity was reduced when the tra2 gene was silenced and the snf gene is essential for oviposition in female. There was no effect on reproduction and female sex determination when silencing the dsx1-like and dsx2-like gene.

CONCLUSION

The genes BTB2, tra2 and snf are involved in oviposition, and ix may be involved in female sex determination and egg formation in Neoseiulus californicus. The results are conductive to further understanding molecular regulatory mechanism of sex determination in predatory mites and may provide a reference for better use of this predatory by producing more females. © 2022 Society of Chemical Industry.

DNA Barcoding and Phylogeny of Acari Species Based on ITS and COI Markers

Acari harbor numerous minute species of agricultural economic importance, mainly Tetranychidae and Phytoseiidae. Great efforts have been established by means of recovering morphological, molecular, and phylogenetic traits for species identification. Traditional identification still relies on external diagnostic characters, which are limited and usually exhibit large phenotypic plasticity within the species, rendering them useless for species delimitation and identification. We decided to increase the number of sequences of the Acari mitochondrial COI (Cytochrome C oxidase I) marker and ITS nuclear ribosomal DNA region for species identification in Tetranychidae and Phytoseiidae. The molecular data allow us to establish species boundaries and phylogenetic relationships among several clades of Acari, mainly Tetranychidae and Phytoseiidae. Sequence comparisons between complete COI and the Acari mitochondrial COI, ITS1-5,8S-ITS2, and ITS2 among all Acari sequences have demonstrated that the selected regions, even small, gave enough informative positions for both species’ identification and phylogenetic studies. Analyses of both DNA regions have unveiled their use as species identification characters, with special emphasis on Acari mitochondrial COI for Tetranychidae and Phytoseiidae species in comparison with the Folmer fragment, which has been universally used as a barcode marker. We demonstrated that the Acari mitochondrial COI region is also a suitable marker to establish a barcode dataset for Acari identification. Our phylogenetic analyses are congruent with other recent works, showing that Acari is a monophyletic group, of which Astigmata, Ixodida, Mesostigmata, Oribatida, and Prostigmata are also monophyletic.

Human follicular mites: Ectoparasites becoming symbionts

Most humans carry mites in the hair follicles of their skin for their entire lives. Follicular mites are the only metazoans tha continuously live on humans. We propose that Demodex folliculorum (Acari) represents a transitional stage from a host-injuring obligate parasite to an obligate symbiont. Here, we describe the profound impact of this transition on the genome and physiology of the mite. Genome sequencing revealed that the permanent host association of D. folliculorum led to an extensive genome reduction through relaxed selection and genetic drift, resulting in the smallest number of protein-coding genes yet identified among panarthropods. Confocal microscopy revealed that this gene loss coincided with an extreme reduction in the number of cells. Single uninucleate muscle cells are sufficient to operate each of the three segments that form each walking leg. While it has been assumed that the reduction of the cell number in parasites starts early in development, we identified a greater total number of cells in the last developmental stage (nymph) than in the terminal adult stage, suggesting that reduction starts at the adult or ultimate stage of development. This is the first evolutionary step in an arthropod species adopting a reductive, parasitic or endosymbiotic lifestyle. Somatic nuclei show underreplication at the diploid stage. Novel eye structures or photoreceptors as well as a unique human host melatonin-guided day/night rhythm are proposed for the first time. The loss of DNA repair genes coupled with extreme endogamy might have set this mite species on an evolutionary dead-end trajectory.

Circulative Transmission of Cileviruses in Brevipalpus Mites May Involve the Paracellular Movement of Virions

Plant viruses transmitted by mites of the genus Brevipalpus are members of the genera Cilevirus, family Kitaviridae, or Dichorhavirus, family Rhabdoviridae. They produce non-systemic infections that typically display necrotic and/or chlorotic lesions around the inoculation loci. The cilevirus citrus leprosis virus C (CiLV-C) causes citrus leprosis, rated as one of the most destructive diseases affecting this crop in the Americas. CiLV-C is vectored in a persistent manner by the flat mite Brevipalpus yothersi. Upon the ingestion of viral particles with the content of the infected plant cell, virions must pass through the midgut epithelium and the anterior podocephalic gland of the mites. Following the duct from this gland, virions reach the salivary canal before their inoculation into a new plant cell through the stylet canal. It is still unclear whether CiLV-C multiplies in mite cells and what mechanisms contribute to its movement through mite tissues. In this study, based on direct observation of histological sections from viruliferous mites using the transmission electron microscope, we posit the hypothesis of the paracellular movement of CiLV-C in mites which may involve the manipulation of septate junctions. We detail the presence of viral particles aligned in the intercellular spaces between cells and the gastrovascular system of Brevipalpus mites. Accordingly, we propose putative genes that could control either active or passive paracellular circulation of viral particles inside the mites.

A dataset of distribution and diversity of blood-sucking mites in China

Mite-borne diseases, such as scrub typhus and hemorrhagic fever with renal syndrome, present an increasing global public health concern. Most of the mite-borne diseases are caused by the blood-sucking mites. To present a comprehensive understanding of the distributions and diversity of blood-sucking mites in China, we derived information from peer-reviewed journal articles, thesis publications and books related to mites in both Chinese and English between 1978 and 2020. Geographic information of blood-sucking mites' occurrence and mite species were extracted and georeferenced at the county level. Standard operating procedures were applied to remove duplicates and ensure accuracy of the data. This dataset contains 6,443 records of mite species occurrences at the county level in China. This geographical dataset provides an overview of the species diversity and wide distributions of blood-sucking mites, and can potentially be used in distribution prediction of mite species and risk assessment of mite-borne diseases in China.

Comparative analysis of mite genomes reveals positive selection for diet adaptation

Diet is a powerful evolutionary force for species adaptation and diversification. Acari is one of the most abundant clades of Arachnida, exhibiting diverse dietary types, while the underlying genetic adaptive mechanisms are not fully understood. Based on comparative analyses of 15 Acari genomes, we found genetic bases for three specialized diets. Herbivores experienced stronger selection pressure than other groups; the olfactory genes and gene families involving metabolizing toxins showed strong adaptive signals. Genes and gene families related to anticoagulation, detoxification, and haemoglobin digestion were found to be under strong selection pressure or significantly expanded in the blood-feeding species. Lipid metabolism genes have a faster evolutionary rate and been subjected to greater selection pressures in fat-feeding species; one positively selected site in the fatty-acid amide hydrolases 2 gene was identified. Our research provides a new perspective for the evolution of Acari and offers potential target loci for novel pesticide development.

A Highly Contiguous Genome Assembly of a Polyphagous Predatory Mite Stratiolaelaps scimitus (Womersley) (Acari: Laelapidae)

As a polyphagous soil-dwelling predatory mite, Stratiolaelaps scimitus (Womersley) (Acari: Laelapidae), formerly known as Stratiolaelaps miles (Berlese), is native to the Northern hemisphere and preys on soil invertebrates, including fungus gnats, springtails, thrips nymphs, nematodes, and other species of mites. Already mass-produced and commercialized in North America, Europe, Oceania and China, S. scimitus will highly likely be introduced to other countries and regions as a biocontrol agent against edaphic pests in the near future. The introduction, however, can lead to unexpected genetic changes within populations of biological control agents, which might decrease the efficacy of pest management or increase the risks to local environments. To better understand the genetic basis of its biology and behavior, we sequenced and assembled the draft genome of S. scimitus using the PacBio Sequel platform II. We generated ∼150× (64.81 Gb) PacBio long reads with an average read length of 12.60 kb. Reads longer than 5 kb were assembled into contigs, resulting in the final assembly of 158 contigs with an N50 length of 7.66 Mb, and captured 93.1% of the BUSCO (Benchmarking Universal Single-Copy Orthologs) gene set (n = 1,066). We identified 16.39% (69.91 Mb) repetitive elements, 1,686 noncoding RNAs, and 13,305 protein-coding genes, which represented 95.8% BUSCO completeness. Combining analyses of genome family evolution and function enrichment of gene ontology and pathway, a total of 135 families experienced significant expansions, which were mainly involved in digestion, detoxification, immunity, and venom. Major expansions of the detoxification enzymes, that is, P450s and carboxylesterases, suggest a possible genetic mechanism underlying polyphagy and ecological adaptions. Our high-quality genome assembly and annotation provide new insights on the evolutionary biology, soil ecology, and biological control for predaceous mites.

Diversity and evolution of the P450 family in arthropods

The P450 family (CYP genes) of arthropods encodes diverse enzymes involved in the metabolism of foreign compounds and in essential endocrine or ecophysiological functions. The P450 sequences (CYPome) from 40 arthropod species were manually curated, including 31 complete CYPomes, and a maximum likelihood phylogeny of nearly 3000 sequences is presented. Arthropod CYPomes are assembled from members of six CYP clans of variable size, the CYP2, CYP3, CYP4 and mitochondrial clans, as well as the CYP20 and CYP16 clans that are not found in Neoptera. CYPome sizes vary from two dozen genes in some parasitic species to over 200 in species as diverse as collembolans or ticks. CYPomes are comprised of few CYP families with many genes and many CYP families with few genes, and this distribution is the result of dynamic birth and death processes. Lineage-specific expansions or blooms are found throughout the phylogeny and often result in genomic clusters that appear to form a reservoir of catalytic diversity maintained as heritable units. Among the many P450s with physiological functions, six CYP families are involved in ecdysteroid metabolism. However, five so-called Halloween genes are not universally represented and do not constitute the unique pathway of ecdysteroid biosynthesis. The diversity of arthropod CYPomes has only partially been uncovered to date and many P450s with physiological functions regulating the synthesis and degradation of endogenous signal molecules (including ecdysteroids) and semiochemicals (including pheromones and defense chemicals) remain to be discovered. Sequence diversity of arthropod P450s is extreme, and P450 sequences lacking the universally conserved Cys ligand to the heme have evolved several times. A better understanding of P450 evolution is needed to discern the relative contributions of stochastic processes and adaptive processes in shaping the size and diversity of CYPomes.

Improving the compatibility of pesticides and predatory mites: recent findings on physiological and ecological selectivity

Integrated pest management relies upon the application of selective pesticides that do not hinder biological control. Phytoseiid mites represent an interesting case-study: they are amongst the most frequently used biological control agents and often are less affected by pesticides than their prey by natural tolerance or by developing resistance. The selectivity of a pesticide is determined by physiological processes that include metabolism, transport, and the affinity to the target-site. Genomic and transcriptomic studies start to elucidate the genetic and molecular mechanisms of differential toxicity in some phytoseiid species, such as a mutation in the sodium channel conferring pyrethroid resistance. Ecological selectivity is achieved by smart applications of pesticides and management practices that influence the persistence of phytoseiid mites on plants. Although modern pesticides often show lower acute toxicity, there is a need for robust assays and procedures that quantify lethal and sublethal effects, through different routes and times of exposure.