Divergent evolutionary trajectories following speciation in two ectoparasitic honey bee mites

Host switch by honey bee parasitic mites leads to symbiont diversification

Host-parasite co-evolution is a reciprocal genetic change; however, the parasite may switch to a novel host, deviating from conventional co-evolution. Varroa destructor is a native parasite of the honey bee Apis cerana, and the mite has established infestation in another honey bee, Apis mellifera, causing colony failure. When mites switched to the novel host, they formed a distinct population from mites that remained on the native host. Consequently, this led to divergence in the microbiota associated with mites in two host populations. The microbes were conserved at the species level reflected by alpha diversity, with substantial relative abundance variance. Microbes found in mites were distinct from the bee microbiota. They mainly were pathogenic with antibiotic resistance, while a few bacterial taxa were previously found in honey bees, including Klebsiella pneumoniae and Pseudomanas aeruginosa. These symbionts may transfer between the mites and honey bees.

The highly improved genome of Ixodes scapularis with X and Y pseudochromosomes

Ixodes scapularis, the black-legged tick, is the principal vector of the Lyme disease spirochete, Borrelia burgdorferi, and is responsible for most of the ∼470,000 estimated Lyme disease cases annually in the USA. Ixodes scapularis can transmit six additional pathogens of human health significance. Because of its medical importance, I. scapularis was the first tick genome to be sequenced and annotated. However, the first assembly, I. scapularis Wikel (IscaW), was highly fragmented because of the technical challenges posed by the long, repetitive genome sequences characteristic of arthropod genomes and the lack of long-read sequencing techniques. Although I. scapularis has emerged as a model for tick research because of the availability of new tools such as embryo injection and CRISPR-Cas9-mediated gene editing yet the lack of chromosome-scale scaffolds has slowed progress in tick biology and the development of tools for their control. Here we combine diverse technologies to produce the I. scapularis Gulia-Nuss (IscGN) genome assembly and gene set. We used DNA from eggs and male and female adult ticks and took advantage of Hi-C, PacBio HiFi sequencing, and Illumina short-read sequencing technologies to produce a chromosome-level assembly. In this work, we present the predicted pseudochromosomes consisting of 13 autosomes and the sex pseudochromosomes: X and Y, and a markedly improved genome annotation compared with the existing assemblies and annotations.

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.

LAMP (Loop-mediated isothermal amplification) assay for rapid identification of Varroa mites

Varroa mites are serious pests of European honeybees (Apis mellifera). For detection of Varroa mite, a new molecular LAMP-based assay has been developed, which retains the body of the mite intact for morphological identification. Six novel Varroa LAMP primers were designed from existing DNA sequences of the COI locus to target V. destructor and V. jacobsoni, providing the ability to tell them apart from other non-target beehive associated mite and insect species. This LAMP assay is specific in detecting these Varroa species and has been tested on specimens originating from multiple countries. It produces amplification of V. destructor and V. jacobsoni in 16 ± 3.4 min with an anneal derivative of 78 ± 0.5 °C whilst another Varroa species,V. underwoodi, showed late amplification. A gBlock gene fragment, used here as a positive control has a different anneal derivative of 80 °C. Three non-destructive DNA extraction methods (HotShot, QuickExtract and Xtract) were tested and found to be suitable for use in the field. The LAMP assay was sensitive to very low levels of Varroa DNA, down to 0.24 picogram (~ 1 × 10 copies/µL of Varroa gBlock). This is a new molecular tool for rapid and accurate detection and identification of Varroa mites for pest management, in areas where these mites do not occur.

Vector-virus interaction affects viral loads and co-occurrence

BACKGROUND

Vector-borne viral diseases threaten human and wildlife worldwide. Vectors are often viewed as a passive syringe injecting the virus. However, to survive, replicate and spread, viruses must manipulate vector biology. While most vector-borne viral research focuses on vectors transmitting a single virus, in reality, vectors often carry diverse viruses. Yet how viruses affect the vectors remains poorly understood. Here, we focused on the varroa mite (Varroa destructor), an emergent parasite that can carry over 20 honey bee viruses, and has been responsible for colony collapses worldwide, as well as changes in global viral populations. Co-evolution of the varroa and the viral community makes it possible to investigate whether viruses affect vector gene expression and whether these interactions affect viral epidemiology.

RESULTS

Using a large set of available varroa transcriptomes, we identified how abundances of individual viruses affect the vector's transcriptional network. We found no evidence of competition between viruses, but rather that some virus abundances are positively correlated. Furthermore, viruses that are found together interact with the vector's gene co-expression modules in similar ways, suggesting that interactions with the vector affect viral epidemiology. We experimentally validated this observation by silencing candidate genes using RNAi and found that the reduction in varroa gene expression was accompanied by a change in viral load.

CONCLUSIONS

Combined, the meta-transcriptomic analysis and experimental results shed light on the mechanism by which viruses interact with each other and with their vector to shape the disease course.

Varroa destructor resistance to tau-fluvalinate: relationship between in vitro phenotypic test and VGSC L925V mutation

BACKGROUND

Varroa destructor is a parasitic mite of the honey bee, Apis mellifera. Its presence in colonies can lead to a collapse within a few years. The use of acaricides has become essential to manage the hive infestation. However, the repeated and possibly incorrect use of acaricide treatments, as tau-fluvalinate, has led to the development of resistance. The in vitro phenotypic test allows the proportion of susceptible or resistant individuals to be known following an exposure to an active substance. In Varroa mites, resistance to tau-fluvalinate is associated with the presence of mutations at the position 925 of the voltage-gated sodium channel (VGSC).

RESULTS

Here, we compared the results obtained with an in vitro phenotypic test against tau-fluvalinate and those obtained with an allelic discrimination assay on 13 treated and untreated Varroa populations in France. The correlation between the phenotype and the genetic profile rate is found to be 0.89 Varroa mites having resistant phenotypic profile have a probability of 63% to present the L925V mutation (resistance detection reliability). However, 97% of the Varroa mites having the susceptible phenotype do not present the L925V mutation (susceptible detection reliability).

CONCLUSION

The L925V mutation explains most of the resistance to tau-fluvalinate in V. destructor in the populations tested. However, other mutations or types of resistance may also be involved to explain the survival of Varroa mites in the phenotypic test. © 2022 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Selection of stable reference genes for quantitative real-time PCR in the Varroa mite, Varroa destructor

To investigate the acaricide toxicity and resistance mechanisms in the Varroa mite, it is essential to understand the genetic responses of Varroa mites to acaricides, which are usually evaluated by transcriptional profiling based on quantitative real-time polymerase chain reaction (qPCR). In this study, to select reference genes showing consistent expression patterns regardless of the acaricide treatment or the type of tissue, Varroa mites treated with each of the three representative acaricides (coumaphos, fluvalinate, and amitraz) were processed for transcriptomic analysis, from which eight genes (NADH dehydrogenase [NADHD], glyceraldehyde-3-phosphate dehydrogenase [GAPDH], eukaryotic translation elongation factor 1 α 1 [eEF1A1], eukaryotic translation elongation factor 2 [eEF2], ribosomal protein L5 [RpL5], Actin, tubulin α-1D chain [α-tubulin], and Rab1) were selected as candidates. The transcription profiles of these genes, depending on the treatment of the three acaricides or across different tissues (cuticle, legs, gut/fat bodies, and synganglion), were analyzed using qPCR with four validation programs, BestKeeper, geNorm, NormFinder, and RefFinder. Following acaricide treatment, eEF1A1 and NADHD showed the least variation in their expression levels, whereas the expression levels of α-tubulin and RpL5 were the most stable across different tissue groups. Rab1/GAPDH and Actin/eEF2 showed the least stable expression patterns following acaricide treatments and across different tissues, respectively, requiring precautions for use. When vitellogenin gene expression was analyzed by different reference genes, its expression profiles varied significantly depending on the reference genes, highlighting the importance of proper reference gene use. Thus, it is recommended using eEF1A1 and NADHD as reference genes for the comparison of the effects of acaricide on the whole body, whereas α-tubulin and RpL5 are recommended for investigating the tissue-specific expression profiles of target genes.

Viral communities in the parasite Varroa destructor and in colonies of their honey bee host (Apis mellifera) in New Zealand

The parasitic mite Varroa destructor is a leading cause of mortality for Western honey bee (Apis mellifera) colonies around the globe. We sought to confirm the presence and likely introduction of only one V. destructor haplotype in New Zealand, and describe the viral community within both V. destructor mites and the bees that they parasitise. A 1232 bp fragment from mitochondrial gene regions suggests the likely introduction of only one V. destructor haplotype to New Zealand. Seventeen viruses were found in bees. The most prevalent and abundant was the Deformed wing virus A (DWV-A) strain, which explained 95.0% of the variation in the viral community of bees. Black queen cell virus, Sacbrood virus, and Varroa destructor virus 2 (VDV-2) played secondary roles. DWV-B and the Israeli acute paralysis virus appeared absent from New Zealand. Ten viruses were observed in V. destructor, with > 99.9% of viral reads from DWV-A and VDV-2. Substantially more variation in viral loads was observed in bees compared to mites. Where high levels of VDV-2 occurred in mites, reduced DWV-A occurred in both the mites and the bees co-occurring within the same hive. Where there were high loads of DWV-A in mites, there were typically high viral loads in bees.

Genomic signatures underlying the oogenesis of the ectoparasitic mite Varroa destructor on its new host Apis mellifera

INTRODUCTION

Host shift of parasites may have devastating effects on the novel hosts. One remarkable example is that of the ectoparasitic mite Varroa destructor, which has shifted its host from Eastern honey bees (Apis cerana) to Western honey bees (Apis mellifera) and posed a global threat to apiculture.

OBJECTIVES

To identify the genetic factors underlying the reproduction of host-shifted V. destructor on the new host.

METHODS

Genome sequencing was conducted to construct the phylogeny of the host-shifted and non-shifted mites and to screen for genomic signatures that differentiated them. Artificial infestation experiment was conducted to compare the reproductive difference between the mites, and transcriptome sequencing was conducted to find differentially expressed genes (DEGs) during the reproduction process.

RESULTS

The host-shifted and non-shifted V. destructor mites constituted two genetically distinct lineages, with 15,362 high-F_ST SNPs identified between them. Oogenesis was upregulated in host-shifted mites on the new host A. mellifera relative to non-shifted mites. The transcriptomes of the host-shifted and non-shifted mites differed significantly as early as 1h post-infestation. The DEGs were associated with nine genes carrying nonsynonymous high-F_ST SNPs, including mGluR2-like, Lamb2-like and Vitellogenin 6-like, which were also differentially expressed, and eIF4G, CG5800, Dap160 and Sas10, which were located in the center of the networks regulating the DEGs based on protein-protein interaction analysis.

CONCLUSIONS

The annotated functions of these genes were all associated with oogenesis. These genes appear to be the key genetic determinants of the oogenesis of host-shifted mites on the new host. Further study of these candidate genes will help elucidate the key mechanism underlying the success of host shifts of V. destructor.

Molecular Detection and Differentiation of Arthropod, Fungal, Protozoan, Bacterial and Viral Pathogens of Honeybees

The honeybee Apis mellifera is highly appreciated worldwide because of its products, but also as it is a pollinator of crops and wild plants. The beehive is vulnerable to infections due to arthropods, fungi, protozoa, bacteria and/or viruses that manage to by-pass the individual and social immune mechanisms of bees. Due to the close proximity of bees in the beehive and their foraging habits, infections easily spread within and between beehives. Moreover, international trade of bees has caused the global spread of infections, several of which result in significant losses for apiculture. Only in a few cases can infections be diagnosed with the naked eye, by direct observation of the pathogen in the case of some arthropods, or by pathogen-associated distinctive traits. Development of molecular methods based on the amplification and analysis of one or more genes or genomic segments has brought significant progress to the study of bee pathogens, allowing for: (i) the precise and sensitive identification of the infectious agent; (ii) the analysis of co-infections; (iii) the description of novel species; (iv) associations between geno- and pheno-types and (v) population structure studies. Sequencing of bee pathogen genomes has allowed for the identification of new molecular targets and the development of specific genotypification strategies.

A derived honey bee stock confers resistance to Varroa destructor and associated viral transmission

The ectoparasite Varroa destructor is the greatest threat to managed honey bee (Apis mellifera) colonies globally. Despite significant efforts, novel treatments to control the mite and its vectored pathogens have shown limited efficacy, as the host remains naïve. A prospective solution lies in the development of Varroa-resistant honey bee stocks, but a paucity of rigorous selection data restricts widespread adoption. Here, we characterise the parasite and viral dynamics of a Varroa-resistant honey bee stock, designated ‘Pol-line’, using a large-scale longitudinal study. Results demonstrate markedly reduced Varroa levels in this stock, diminished titres of three major viruses (DWV-A, DWV-B, and CBPV), and a two-fold increase in survival. Levels of a fourth virus that is not associated with Varroa—BQCV—do not differ between stocks, supporting a disruption of the transmission pathway. Further, we show that when decoupled from the influence of Varroa levels, viral titres do not constitute strong independent predictors of colony mortality risk. These findings highlight the need for a reassessment of Varroa etiology, and suggest that derived stocks represent a tractable solution to the Varroa pandemic.

An Insight Into the microRNA Profile of the Ectoparasitic Mite Varroa destructor (Acari: Varroidae), the Primary Vector of Honey Bee Deformed Wing Virus

The remarkably adaptive mite Varroa destructor is the most important honey bee ectoparasite. Varroa mites are competent vectors of deformed wing virus (DWV), and the Varroa-virus complex is a major determinant of annual honey bee colony mortality and collapse. MicroRNAs (miRNAs) are 22-24 nucleotide non-coding RNAs produced by all plants and animals and some viruses that influence biological processes through post-transcriptional regulation of gene expression. Knowledge of miRNAs and their function in mite biology remains limited. Here we constructed small RNA libraries from male and female V. destructor using Illumina's small RNA-Seq platform. A total of 101,913,208 and 91,904,732 small RNA reads (>18 nucleotides) from male and female mites were analyzed using the miRDeep2 algorithm. A conservative approach predicted 306 miRNAs, 18 of which were upregulated and 13 downregulated in female V. destructor compared with males. Quantitative real-time PCR validated the expression of selected differentially-expressed female Varroa miRNAs. This dataset provides a list of potential miRNA targets involved in regulating vital Varroa biological processes and paves the way for developing strategies to target Varroa and their viruses.

Green Veterinary Pharmacology for Honey Bee Welfare and Health: Origanum heracleoticum L. (Lamiaceae) Essential Oil for the Control of the Apis mellifera Varroatosis

Varroatosis, caused by the Varroa destructor mite, is currently the most dangerous parasitic disease threatening the survival of honey bees worldwide. Its adverse effect on the welfare and health of honey bees requires the regular use of specific acaricides. This condition has led to a growing development of resistance phenomena towards the most frequently used drugs. In addition, another important aspect that should not be understated, is the toxicity and persistence of chemicals in the environment. Therefore, the identification of viable and environmentally friendly alternatives is urgently needed. In this scenario, essential oils are promising candidates. The aim of this study was to assess the contact toxicity, the fumigation efficacy and the repellent effect of Origanum heracleoticum L. essential oil (EO) against V. destructor mite. In the contact tests, each experimental replicate consisted of 15 viable adult female mites divided as follows: 5 treated with EO diluted in HPLC grade acetone, 5 treated with acetone alone (as negative control) and 5 treated with Amitraz diluted in acetone (as positive control). The EO was tested at concentrations of 0.125, 0.25, 0.5, 1 and 2 mg/mL. For each experimental replicate, mortality was manually assessed after one hour. The efficacy of EO fumigation was evaluated through prolonged exposure at different time intervals. After each exposure, the 5 mites constituting an experimental replicate were transferred to a Petri dish containing a honey bee larva and mortality was assessed after 48 h. The repellent action was investigated by implementing a directional choice test in a mandatory route. During the repellency tests the behavior of the mite (90 min after its introduction in the mandatory route) was not influenced by the EO. In contact tests, EO showed the best efficacy at 2 and 1 mg/mL concentrations, neutralizing (dead + inactivated) 90.9% and 80% of the mites, respectively. In fumigation tests, the mean mortality rate of V. destructor at maximum exposure time (90 min) was 60% and 84% at 24 and 48 h, respectively. Overall, these results demonstrate a significant efficacy of O. heracleoticum EO against V. destructor, suggesting a possible alternative use in the control of varroatosis in honey bee farms in order to improve Apis mellifera welfare and health and, consequently, the hive productions.

The first steps toward a global pandemic: Reconstructing the demographic history of parasite host switches in its native range

Host switching allows parasites to expand their niches. However, successful switching may require suites of adaptations and also may decrease performance on the old host. As a result, reductions in gene flow accompany many host switches, driving speciation. Because host switches tend to be rapid, it is difficult to study them in real-time, and their demographic parameters remain poorly understood. As a result, fundamental factors that control subsequent parasite evolution, such as the size of the switching population or the extent of immigration from the original host, remain largely unknown. To shed light on the host switching process, we explored how host switches occur in independent host shifts by two ectoparasitic honey bee mites (Varroa destructor and V. jacobsoni). Both switched to the western honey bee (Apis mellifera) after being brought into contact with their ancestral host (Apis cerana), ~70 and ~12 years ago, respectively. Varroa destructor subsequently caused worldwide collapses of honey bee populations. Using whole-genome sequencing on 63 mites collected in their native ranges from both the ancestral and novel hosts, we were able to reconstruct the known temporal dynamics of the switch. We further found multiple previously undiscovered mitochondrial lineages on the novel host, along with the genetic equivalent of tens of individuals that were involved in the initial host switch. Despite being greatly reduced, some gene flow remains between mites adapted to different hosts. Our findings suggest that while reproductive isolation may facilitate the fixation of traits beneficial for exploiting the new host, ongoing genetic exchange may allow genetic amelioration of inbreeding effects.

De novo transcriptome sequencing of the northern fowl mite, Ornithonyssus sylviarum, shed light on parasitiform poultry mites evolution and its chemoreceptor repertoires

The northern fowl mite (NFM), Ornithonyssus sylviarum, and the poultry red mite (PRM), Dermanyssus gallinae, are the most serious pests of poultry, both of which have an expanding global prevalence. Research on NFM has been constrained by a lack of genomic and transcriptomic data. Here, we report and analyze the first global transcriptome data across all mite live stages and sexes. A total of 28,999 unigenes were assembled, of which 19,750 (68.10%) were annotated using seven functional databases. The biological function of these unigenes was classified using the GO, KOG, and KEGG databases. To gain insight into the chemosensory receptor-based system of parasitiform mites, we furthermore assessed the gene repertoire of gustatory receptors (GRs) and ionotropic receptors (IRs), both of which encode putative ligand-gated ion channel proteins. While these receptors are well characterized in insect model species, our understanding of chemosensory detection in mites and ticks is in its infancy. To address this paucity of data, we identified 9 IR/iGluRs and 2 GRs genes by analyzing transcriptome data in the NFM, while 9 GRs and 41 IR/iGluRs genes were annotated in the PRM genome. Taken together, the transcriptomic and genomic annotation of these two species provide a valuable reference for studies of parasitiform mites and also help to understand how chemosensory gene family expansion/contraction events may have been reshaped by an obligate parasitic lifestyle compared with their free-living closest relatives. Future studies should include additional species to validate this observation and functional characterization of the identified proteins as a step forward in identifying tools for controlling these poultry pests.

Understanding the Enemy: A Review of the Genetics, Behavior and Chemical Ecology of Varroa destructor, the Parasitic Mite of Apis mellifera

Varroa destructor (Mesostigmata: Varroidae) is arguably the most damaging parasitic mite that attacks honey bees worldwide. Since its initial host switch from the Asian honey bee (Apis cerana) (Hymenoptera: Apidae) to the Western honey bee (Apis mellifera) (Hymenoptera: Apidae), Varroa has become a widely successful invasive species, attacking honey bees on almost every continent where apiculture is practiced. Two haplotypes of V. destructor (Japanese and Korean) parasitize A. mellifera, both of which vector various honey bee-associated viruses. As the population of Varroa grows within a colony in the spring and summer, so do the levels of viral infections. Not surprisingly, high Varroa parasitization impacts bees at the individual level, causing bees to exhibit lower weight, decreased learning capacity, and shorter lifespan. High levels of Varroa infestation can lead to colony-wide varroosis and eventually colony death, especially when no control measures are taken against the mites. Varroa has become a successful parasite of A. mellifera because of its ability to reproduce within both drone cells and worker cells, which allows populations to expand rapidly. Varroa uses several chemical cues to complete its life cycle, many of which remain understudied and should be further explored. Given the growing reports of pesticide resistance by Varroa in several countries, a better understanding of the mite's basic biology is needed to find alternative pest management strategies. This review focuses on the genetics, behavior, and chemical ecology of V. destructor within A. mellifera colonies, and points to areas of research that should be exploited to better control this pervasive honey bee enemy.

Haplotype Analysis of Varroa destructor and Deformed Wing Virus Using Long Reads

As a phoretic parasite and virus vector, the mite Varroa destructor and the associated Deformed wing virus (DWV) form a lethal combination to the honey bee, Apis mellifera. Routine acaricide treatment has been reported to reduce the diversity of mites and select for tolerance against these treatments. Further, different DWV strains face selective pressures when transmitted via mites. In this study, the haplotypes of Varroa mites and associated DWV variants were quantified using long reads. A single haplotype dominated the mite mitochondrial gene cytochrome oxidase subunit I, reflecting an ancient bottleneck. However, highly polymorphic genes were present across the mite genome, suggesting the diversity of mites could be actively maintained at a regional level. DWV detected in both mites and honey bees show a dominant variant with only a few low-frequency alternate haplotypes. The relative abundances of DWV haplotypes isolated from honey bees and mites were highly consistent, suggesting that some variants are favored by ongoing selection.

A gene drive does not spread easily in populations of the honey bee parasite Varroa destructor

Varroa mites (Varroa destructor) are the most significant threat to beekeeping worldwide. They are directly or indirectly responsible for millions of colony losses each year. Beekeepers are somewhat able to control varroa populations through the use of physical and chemical treatments. However, these methods range in effectiveness, can harm honey bees, can be physically demanding on the beekeeper, and do not always provide complete protection from varroa. More importantly, in some populations varroa mites have developed resistance to available acaricides. Overcoming the varroa mite problem will require novel and targeted treatment options. Here, we explore the potential of gene drive technology to control varroa. We show that spreading a neutral gene drive in varroa is possible but requires specific colony-level management practices to overcome the challenges of both inbreeding and haplodiploidy. Furthermore, continued treatment with acaricides is necessary to give a gene drive time to fix in the varroa population. Unfortunately, a gene drive that impacts female or male fertility does not spread in varroa. Therefore, we suggest that the most promising way forward is to use a gene drive which carries a toxin precursor or removes acaricide resistance alleles.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s13592-021-00891-5.

Reduced proinsecticide activation by cytochrome P450 confers coumaphos resistance in the major bee parasite Varroa destructor

Varroa destructor is one of the main problems in modern beekeeping. Highly selective acaricides with low toxicity to bees are used internationally to control this mite. One of the key acaricides is the organophosphorus (OP) proinsecticide coumaphos, that becomes toxic after enzymatic activation inside Varroa We show here that mites from the island Andros (AN-CR) exhibit high levels of coumaphos resistance. Resistance is not mediated by decreased coumaphos uptake, target-site resistance, or increased detoxification. Reduced proinsecticide activation by a cytochrome P450 enzyme was the main resistance mechanism, a powerful and rarely encountered evolutionary solution to insecticide selection pressure. After treatment with sublethal doses of [¹⁴C] coumaphos, susceptible mite extracts had substantial amounts of coroxon, the activated metabolite of coumaphos, while resistant mites had only trace amounts. This indicates a suppression of the P450 (CYP)-mediated activation step in the AN-CR mites. Bioassays with coroxon to bypass the activation step showed that resistance was dramatically reduced. There are 26 CYPs present in the V. destructor genome. Transcriptome analysis revealed overexpression in resistant mites of CYP4DP24 and underexpression of CYP3012A6 and CYP4EP4 RNA interference of CYP4EP4 in the susceptible population, to mimic underexpression seen in the resistant mites, prevented coumaphos activation and decreased coumaphos toxicity.

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.

qPCR assays with dual-labeled probes for genotyping honey bee variants associated with varroa resistance

Background

The varroa mite is one of the main causes of honey bee mortality. An important mechanism by which honey bees increase their resistance against this mite is the expression of suppressed mite reproduction. This trait describes the physiological inability of mites to produce viable offspring and was found associated with eight genomic variants in previous research.

Results

This paper presents the development and validation of high-throughput qPCR assays with dual-labeled probes for discriminating these eight single-nucleotide variants. Amplicon sequences used for assay validation revealed additional variants in the primer/probe binding sites in four out of the eight assays. As for two of these the additional variants interfered with the genotyping outcome supplementary primers and/or probes were developed. Inclusion of these primers and probes in the assay mixes allowed for the correct genotyping of all eight variants of interest within our bee population.

Conclusion

These outcomes underline the importance of checking for interfering variants in designing qPCR assays. Ultimately, the availability of this assay allows genotyping for the suppressed mite reproduction trait and paves the way for marker assisted selection in breeding programs.

Adaptation to vector-based transmission in a honeybee virus

Global pollinator declines as a result of emerging infectious diseases are of major concern. Managed honeybees Apis mellifera are susceptible to numerous parasites and pathogens, many of which appear to be transmissible to sympatric non-Apis taxa. The ectoparasitic mite Varroa destructor is considered to be the most significant threat to honeybees due to its role in vectoring RNA viruses, particularly Deformed wing virus (DWV). Vector transmission of DWV has resulted in the accumulation of high viral loads in honeybees and is often associated with colony death. DWV has two main genotypes, A and B. DWV-A was more prevalent during the initial phase of V. destructor establishment. In recent years, the global prevalence of DWV-B has increased, suggesting that DWV-B is better adapted to vector transmission than DWV-A. We aimed to determine the role vector transmission plays in DWV genotype prevalence at a colony level. We experimentally increased or decreased the number of V. destructor mites in honeybee colonies, and tracked DWV-A and DWV-B loads over a period of 10 months. Our results show that the two DWV genotypes differ in their response to mite numbers. DWV-A accumulation in honeybees was positively correlated with mite numbers yet DWV-A was largely undetected in the absence of the mite. In contrast, colonies had high loads of DWV-B even when mite numbers were low. DWV-B loads persisted in miticide-treated colonies, indicating that this genotype has a competitive advantage over DWV-A irrespective of mite numbers. Our findings suggest that the global increase in DWV-B prevalence is not driven by selective pressure by the vector. Rather, DWV-B is able to persist in colonies at higher viral loads relative to DWV-A in the presence and absence of V. destructor. The interplay between V. destructor and DWV genotypes within honeybee colonies may have broad consequences upon viral diversity in sympatric taxa as a result of spillover.

Investigation of circular RNAs in an ectoparasitic mite Varroa destructor (Acarina: Varroidae) of the honey bee

Circular RNAs (circRNAs) are a large class of non-protein-coding transcripts that are involved in a diverse spectrum of regulatory mechanisms across a broad range of biological processes. To date, however, few studies on circRNAs have investigated their role in the biology of invertebrate parasites. The ectoparasitic mite Varroa destructor is perceived as the principal biotic threat towards global honey bee health. This parasite cannot be sustainably controlled partially due to the lack of knowledge about its basic molecular biology. In this paper, we unveil the circRNA profile of V. destructor for the first time and report the sources, distribution, and features of the identified circRNAs. Exonic, intronic, exon-intron, and intergenic circRNAs were discovered and exon-intron circRNAs were the most abundant within the largest spliced length. Three hundred and eighty-six (8.3%) circRNAs were predicted to possess translational potential. Eleven circRNAs, derived from six parental genes, exhibited strong bonds with miRNAs as sponges, suggesting an efficient post-transcriptional regulation. GO term and KEGG pathway enrichment analyses of the parental genes of the identified circRNAs showed that these non-coding RNAs were mainly engaged in protein processing, signal transduction, and various metabolism processes. To our knowledge, this is the first catalog of a circRNA profile of parasitiformes species, which reveals the prevalence of circRNAs in the parasite and provides biological insights for future genetic studies on this ubiquitous parasitic mite.

A toolkit for studying Varroa genomics and transcriptomics: preservation, extraction, and sequencing library preparation

BACKGROUND

The honey bee parasite, Varroa destructor, is a leading cause of honey bee population declines. In addition to being an obligate ectoparasitic mite, Varroa carries several viruses that infect honey bees and act as the proximal cause of colony collapses. Nevertheless, until recently, studies of Varroa have been limited by the paucity of genomic tools. Lab- and field-based methods exploiting such methods are still nascent. This study developed a set of methods for preserving Varroa DNA and RNA from the field to the lab and processing them into sequencing libraries. We performed preservation experiments in which Varroa mites were immersed in TRIzol, RNAlater, and absolute ethanol for preservation periods up to 21 days post-treatment to assess DNA and RNA integrity.

RESULTS

For both DNA and RNA, mites preserved in TRIzol and RNAlater at room temperature degraded within 10 days post-treatment. Mites preserved in ethanol at room temperature and 4 °C remained intact through 21 days. Varroa mite DNA and RNA libraries were created and sequenced for ethanol preserved samples, 15 and 21 days post-treatment. All DNA sequences mapped to the V. destructor genome at above 95% on average, while RNA sequences mapped to V. destructor, but also sometimes to high levels of the deformed-wing virus and to various organisms.

CONCLUSIONS

Ethanolic preservation of field-collected mites is inexpensive and simple, and allows them to be shipped and processed successfully in the lab for a wide variety of sequencing applications. It appears to preserve RNA from both Varroa and at least some of the viruses it vectors.

Juvenile hormone pathway in honey bee larvae: A source of possible signal molecules for the reproductive behavior of Varroa destructor

The parasitic mite Varroa destructor devastates honey bee (Apis mellifera) colonies around the world. Entering a brood cell shortly before capping, the Varroa mother feeds on the honey bee larvae. The hormones 20-hydroxyecdysone (20E) and juvenile hormone (JH), acquired from the host, have been considered to play a key role in initiating Varroa's reproductive cycle. This study focuses on differential expression of the genes involved in the biosynthesis of JH and ecdysone at six time points during the first 30 hr after cell capping in both drone and worker larvae of A. mellifera. This time frame, covering the conclusion of the honey bee brood cell invasion and the start of Varroa's ovogenesis, is critical to the successful initiation of a reproductive cycle. Our findings support a later activation of the ecdysteroid cascade in honey bee drones compared to worker larvae, which could account for the increased egg production of Varroa in A. mellifera drone cells. The JH pathway was generally downregulated confirming its activity is antagonistic to the ecdysteroid pathway during the larva development. Nevertheless, the genes involved in JH synthesis revealed an increased expression in drones. The upregulation of jhamt gene involved in methyl farnesoate (MF) synthesis came into attention since the MF is not only a precursor of JH but it is also an insect pheromone in its own right as well as JH-like hormone in Acari. This could indicate a possible kairomone effect of MF for attracting the mites into the drone brood cells, along with its potential involvement in ovogenesis after the cell capping, stimulating Varroa's initiation of egg laying.

A genome-wide screening for RNAi pathway proteins in Acari

BACKGROUND

RNA interference (RNAi) is a highly conserved, sequence-specific gene silencing mechanism present in Eukaryotes. Three RNAi pathways are known, namely micro-RNA (miRNA), piwi-interacting RNA (piRNA) and short interfering RNA (siRNA). However, little knowledge exists about the proteins involved in these pathways in Acari. Moreover, variable successes has been obtained in gene knockdown via siRNA pathway in their functional genomics and management. We hypothesized that the clue may be in the variability of the composition and the efficacy of siRNA machinery among Acari.

RESULTS

Both comparative genomic analyses and domain annotation suggest that all the analyzed species have homologs of putative core proteins that mediate cleaving of targeted genes via the three RNAi pathways. We identified putative homologs of Caenorhabditis elegans RNA-dependent RNA polymerase (RdRP) protein in all species though no secondary Argonaute homologs that operate with this protein in siRNA amplification mechanism were found, suggesting that the siRNA amplification mechanism present in Acari may be distinct from that described in C. elegans. Moreover, the genomes of these species do not encode homologs of C. elegans systemic RNAi defective-1 (Sid-1) protein that mediate silencing of the mRNA target throughout the treated organisms suggesting that the phenomena of systemic RNAi that has been reported in some Acari species probably occur through a different mechanism. However, homologs of putative RNAi spreading defective-3 (Rsd-3) protein and scavenger receptors namely Eater and SR-CI that mediate endocytosis cellular update of dsRNA in C. elegans and Drosophila melanogaster were found in Acari genomes. This result suggests that cellular dsRNA uptake in Acari is endocytosis-dependent. Detailed phylogenetic analyses of core RNAi pathway proteins in the studied species revealed that their evolution is compatible with the proposed monophyletic evolution of this group.

CONCLUSIONS

Our analyses have revealed the potential activity of all three pathways in Acari. Still, much experimental work remains to be done to confirm the mechanisms behind these pathways in particular those that govern systemic/parental RNAi and siRNA amplification in Acari. Disclosure of these mechanisms will facilitate the development of new and specific management tools for the harmful species and enrichment of the beneficial species.

Elevated rates of positive selection drive the evolution of pestiferousness in the Colorado potato beetle (Leptinotarsa decemlineata, Say)

Contextualizing evolutionary history and identifying genomic features of an insect that might contribute to its pest status is important in developing early detection and control tactics. In order to understand the evolution of pestiferousness, which we define as the accumulation of traits that contribute to an insect population's success in an agroecosystem, we tested the importance of known genomic properties associated with rapid adaptation in the Colorado potato beetle (CPB), Leptinotarsa decemlineata Say. Within the leaf beetle genus Leptinotarsa, only CPB, and a few populations therein, has risen to pest status on cultivated nightshades, Solanum. Using whole genomes from ten closely related Leptinotarsa species native to the United States, we reconstructed a high-quality species tree and used this phylogenetic framework to assess evolutionary patterns in four genomic features of rapid adaptation: standing genetic variation, gene family expansion and contraction, transposable element abundance and location, and positive selection at protein-coding genes. Throughout approximately 20 million years of history, Leptinotarsa species show little evidence of gene family turnover and transposable element variation. However, there is a clear pattern of CPB experiencing higher rates of positive selection on protein-coding genes. We determine that these rates are associated with greater standing genetic variation due to larger effective population size, which supports the theory that the demographic history contributes to rates of protein evolution. Furthermore, we identify a suite of coding genes under positive selection that are putatively associated with pestiferousness in the Colorado potato beetle lineage. They are involved in the biological processes of xenobiotic detoxification, chemosensation and hormone function.

Varroa destructor: how does it harm Apis mellifera honey bees and what can be done about it?

Since its migration from the Asian honey bee (Apis cerana) to the European honey bee (Apis mellifera), the ectoparasitic mite Varroa destructor has emerged as a major issue for beekeeping worldwide. Due to a short history of coevolution, the host–parasite relationship between A. mellifera and V. destructor is unbalanced, with honey bees suffering infestation effects at the individual, colony and population levels. Several control solutions have been developed to tackle the colony and production losses due to Varroa, but the burden caused by the mite in combination with other biotic and abiotic factors continues to increase, weakening the beekeeping industry. In this synthetic review, we highlight the main advances made between 2015 and 2020 on V. destructor biology and its impact on the health of the honey bee, A. mellifera. We also describe the main control solutions that are currently available to fight the mite and place a special focus on new methodological developments, which point to integrated pest management strategies for the control of Varroa in honey bee colonies.

Genome-Wide Identification of Long Non-coding RNAs in the Gravid Ectoparasite Varroa destructor

Long non-coding RNAs (lncRNAs) emerge as critical regulators across a wide variety of biological functions in living organisms. However, to date, no systematic characterization of lncRNAs has been investigated in the ectoparasitic mite Varroa destructor, the most severe biotic threat to honey bees worldwide. Here, we performed an initial genome-wide identification of lncRNAs in V. destructor via high-throughput sequencing technology and reported, for the first time, the transcriptomic landscape of lncRNAs in the devastating parasite. By means of a lncRNA identification pipeline, 6,645 novel lncRNA transcripts, encoded by 3,897 gene loci, were identified, including 2,066 sense lncRNAs, 2,772 lincRNAs, and 1,807 lncNATs. Compared with protein-coding mRNAs, V. destructor lncRNAs are shorter in terms of full length, as well as of the ORF length, contain less exons, and express at lower level. GO term and KEGG pathway enrichment analyses of the lncRNA target genes demonstrated that these predicted lncRNAs may be potentially responsible for the regulatory functions of cellular and biological progresses in the reproductive phase of V. destructor. To our knowledge, this is the first catalog of lncRNA profile in the parasitiformes species, providing a valuable resource for genetic and genomic studies. Understanding the characteristics and features of lncRNAs in V. destructor would promote sustainable parasite control.

Evaluation of Suppressed Mite Reproduction (SMR) Reveals Potential for Varroa Resistance in European Honey Bees (Apis mellifera L.)

Simple Summary

The mite Varroa destructor represents a great threat to honey bees and the beekeeping industry. The opportunity to select and breed honey bees that are naturally able to fight the mite stands a sustainable solution. This can be achieved by evaluation of the failure of mite reproduction (SMR, suppressed mite reproduction). We conducted a large European experiment to assess the SMR trait in different populations of honey bees spread over 13 different countries, and representing different honey bee populations. The first goal was to standardize and validate the SMR evaluation method, and then to compare the SMR trait between the different populations. Our results indicate that it is necessary to examine at least 35 brood cells infested by a single mite to reliably estimate the SMR score of any given colony. Several colonies from our dataset display high SMR scores, indicating that this trait is present within the European honey bee populations. No major differences could be identified between countries for a given population, or between populations in different countries. This study shows the potential to increase selection efforts to breed V. destructor honey bee resistant populations.

Abstract

In the fight against the Varroa destructor mite, selective breeding of honey bee (Apis mellifera L.) populations that are resistant to the parasitic mite stands as a sustainable solution. Selection initiatives indicate that using the suppressed mite reproduction (SMR) trait as a selection criterion is a suitable tool to breed such resistant bee populations. We conducted a large European experiment to evaluate the SMR trait in different populations of honey bees spread over 13 different countries, and representing different honey bee genotypes with their local mite parasites. The first goal was to standardize and validate the SMR evaluation method, and then to compare the SMR trait between the different populations. Simulation results indicate that it is necessary to examine at least 35 single-infested cells to reliably estimate the SMR score of any given colony. Several colonies from our dataset display high SMR scores indicating that this trait is present within the European honey bee populations. The trait is highly variable between colonies and some countries, but no major differences could be identified between countries for a given genotype, or between genotypes in different countries. This study shows the potential to increase selective breeding efforts of V. destructor resistant populations.

Inventory of Varroa destructor susceptibility to amitraz and tau-fluvalinate in France

Varroa destructor is one of the greatest threats for the European honeybee, Apis mellifera. Acaricides are required to control mite infestation. Three conventional chemical acaricide substances are used in France: tau-fluvalinate, flumethrin and amitraz. Tau-fluvalinate was used for over 10 years before experiencing a loss of effectiveness. In 1995, bioassay trials showed the first mite resistance to tau-fluvalinate. In some countries, amitraz was widely used, also leading to resistance of V. destructor to amitraz. In France, some efficiency field tests showed a loss of treatment effectiveness with amitraz. We adapted the bioassay from Maggi and collaborators to determine mite susceptibility to tau-fluvalinate and amitraz in France in 2018 and 2019. The lethal concentration (LC) which kills 90% of susceptible mite strains (LC₉₀) is 0.4 and 12 µg/mL for amitraz and tau-fluvalinate, respectively. These concentrations were chosen as the determining factors to evaluate mite susceptibility. Some mites, collected from different apiaries, present resistance to amitraz and tau-fluvalinate (71% of the mite samples show resistance to amitraz and 57% to tau-fluvalinate). As there are few active substances available in France, and if mite resistance to acaricides continues to increase, the effectiveness of the treatments will decrease and therefore more treatments per year will be necessary. To prevent this situation, a new strategy needs to be put in place to include mite resistance management. We suggest that a bioassay would be a good tool with which to advise the policymakers.

Varroa mite evolution: a neglected aspect of worldwide bee collapses?

While ectoparasitic Varroa mites cause minimal damage to their co-evolved ancestral host, the eastern honey bee (Apis cerana), they devastate their novel host, the western honey bee (Apis mellifera). Over several decades, the host switch caused worldwide population collapses, threatening global food security. Varroa management strategies have focused on breeding bees for tolerance. But, can Varroa overcome these counter-adaptations in a classic coevolutionary arms race? Despite increasing evidence for Varroa genetic diversity and evolvability, this eventuality has largely been neglected. We therefore suggest a more holistic paradigm for studying this host-parasite interaction, one in which 'Varroa-tolerant' bee traits should be viewed as a shared phenotype resulting from Varroa and honey bee interaction.

Varroa destructor: A Complex Parasite, Crippling Honey Bees Worldwide

The parasitic mite, Varroa destructor, has shaken the beekeeping and pollination industries since its spread from its native host, the Asian honey bee (Apis cerana), to the naïve European honey bee (Apis mellifera) used commercially for pollination and honey production around the globe. Varroa is the greatest threat to honey bee health. Worrying observations include increasing acaricide resistance in the varroa population and sinking economic treatment thresholds, suggesting that the mites or their vectored viruses are becoming more virulent. Highly infested weak colonies facilitate mite dispersal and disease transmission to stronger and healthier colonies. Here, we review recent developments in the biology, pathology, and management of varroa, and integrate older knowledge that is less well known.

Reproduction of Distinct Varroa destructor Genotypes on Honey Bee Worker Brood

Honey bees play important roles in pollination for many crops and wild plants, but have been facing great threats posed by various pathogens and parasites. Among them, Varroa destructor, an obligate ectoparasite of honey bees, is considered the most damaging. Within the last century, V. destructor shifted from the original host, the Asian honey bee Apis cerana to the new host, the European honey bee A. mellifera. However, the reproduction of Varroa mites, especially of different haplotypes in the two hosts, is still largely unknown. In this study, we first investigated the existing Varroa haplotypes in local colonies in southern China, and then compared the reproduction of different haplotypes on the worker brood of both the original and new hosts by artificial inoculation. We confirmed that there are two haplotypes of V. destructor in southern China, one is the Korea haplotype and the other is the China haplotype, and the two types parasitized different honey bee species. Although Varroa females from A. mellifera (Korea haplotype) are able to reproduce on the worker brood of both honey bee species, they showed better reproductive performance in the new host A. mellifera with significantly higher fecundity (number of offspring per mother mite) and reproductive rate (number of adult daughters per mother mite), suggesting that this parasite gains higher fitness after host shift. The data further showed that a short stay of Varroa females inside the A. cerana worker cells decreased their fecundity and especially the reproductive rate in a time-dependent manner, suggesting that the A. cerana worker cells may inhibit Varroa reproduction. In contrast, Varroa mites derived from A. cerana colonies (China haplotype) were entirely sterile in A. mellifera worker cells during two sequential inoculations, while the control mites from A. mellifera colonies (Korea haplotype) reproduced normally. In addition, all the infertile mites were found to defecate on the abdomen of bee pupae. We have revealed that two haplotypes of V. destructor exhibit differential reproduction on the worker brood of the original and new host honey bees, providing novel insights into the diversity and complexity of the reproduction of V. destructor.