Biology subjects

Ashe, A.

Publications and source records attributed to Ashe, A..

7 recordsLinked to original sources

bioRxiv2026

Primary and secondary antiviral RNAi responses throughout Varroa destructor life stages reveal the vertical transmission of viruses

One of the most devastating threats to global honey bee health is the ectoparasitic mite and viral vector Varroa destructor, yet the transmission dynamics of viruses carried by mites are poorly understood. RNA interference (RNAi) is a major antiviral defence mechanism in invertebrates including Varroa, where actively replicating viruses are degraded into virus-derived small interfering RNAs (vsiRNAs). Insects typically produce 20-22 nt vsiRNAs with sense and antisense polarity, however established viral infections in V. destructor lead to the production of 24-nt antisense vsiRNA fragments, which could indicate the presence of secondary siRNA synthesis. To better understand viral infection and transmission dynamics in V. destructor, we conducted small RNA sequencing of male and female mites throughout development, from egg to reproductive stages. Viral community structure was largely driven by developmental stage, with younger and older life stages clustering separately. We identified five viruses that are consistently degraded into antisense 24-nt vsiRNA across all developmental stages, suggesting that these viruses are transmitted vertically and form part of Varroas core virome. This includes the highly diverse Varroa destructor virus 2 (VDV-2), for which we observe eight distinct VDV-2 strains that simultaneously co-infect individual mites throughout development. In contrast, sense and antisense 23-nt vsiRNA fragments are generated in response to the honey bee pathogen, Iflavirus aladeformis (deformed wing virus A, DWV-A) in eggs, but the vsiRNA size profile transitions to 24-nt antisense fragments at later life stages. Our results suggest that once a virus is first acquired by Varroa, a primary 23-nt sense and antisense antiviral response precedes the production of secondary 24-nt antisense vsiRNAs as the infection progresses. We confirm this observation using synthetic dsRNA, which show both primary and secondary siRNA processing, revealing how exogenous dsRNA processing occurs in Varroa. These results show distinct primary and secondary antiviral RNAi responses across V. destructor life stages and demonstrate how vsiRNA profiles can be used to infer virus transmission routes and long-term persistence within vector populations.

genetics↗

bioRxiv2026

Holistic meta-analysis of Caenorhabditis elegans germ granule proteomics reveals complex dynamics and new candidate granule associated proteins

Spatiotemporal organisation of biological molecules is a key driver of cellular processes, including many post-transcriptional epigenetic processes. The germline-specific germ granules are biomolecular condensates that act as hubs for mRNA and small RNA processing and are core regulators of germline gene expression programming. Germ granules have been studied extensively in C. elegans, and recent developments have led to many subdivisions of the germ granule into specialised compartments. Rapid advancements in microscopy and protein-protein interaction (PPI) screening techniques have produced a large amount of data towards characterising the localisation of proteins to specific granules. However, common methods used to probe PPIs are limited in their ability to robustly detect valid interactions, especially the multivalent and sometimes transient ones observed in granule environments. Here we perform a meta-analysis of granule protein interaction screens. While these experiments generally enrich for proteins matching the profile of granule-associated proteins, we find that when considering screens individually, reproducibility is surprisingly low, highlighting not only the variability inherent in these methods but also the dynamic nature of the PPI networks present in granules. We developed an algorithm to provide a measure of each proteins association with specific granules across various experiments. By further clustering and investigation of the resulting score matrix, we demonstrate the power of this holistic approach to provide deeper insights into germ granule organisation and highlight novel can provide a resource to better inform future investigations into granules and their constituent proteins.

genetics↗

bioRxiv2025

Conserved but mechanistically diverse piRNA defence against gypsy LTR retrotransposons in insect ovaries

Organisms have evolved highly adaptable defence systems to silence mobile genetic elements such as transposons. While individual transposons may emerge and vanish over time, the long-term evolutionary stability of the pathways that suppress them remains poorly understood. In the ovarian somatic cells of Drosophila, envelope-carrying gypsy long terminal repeat (LTR) retrotransposons are silenced by the Piwi-interacting RNA (piRNA) pathway, which depends exclusively on Piwi - an evolutionary derivative of an Aubergine/Piwi gene duplication unique to flies. Recent studies, however, have revealed that envelope-carrying gypsy elements are widespread across metazoans and particularly abundant in insect genomes, raising questions about the origin of ovarian somatic piRNA defence. Here we demonstrate that Aedes and Anopheles mosquitoes, as well as stingless bees and crickets, all produce piRNAs targeting gypsy elements in ovarian somatic cells, indicating a continuous arms race in this cellular niche for more than 400 million years of insect evolution. Notably, in Aedes aegypti, ovarian somatic cells express the same piRNA clusters as other somatic tissues, where they are known to target RNA viruses - suggesting a shared origin of anti-viral and anti-retrotransposon defences. Furthermore, we reveal striking lineage-specific differences in ovarian somatic piRNA biogenesis: slicing-independent phasing dominates in dipterans, ping-pong amplification in bees, and slicing-dependent phasing in crickets. Together, these findings indicate that distinct piRNA pathways have independently evolved at different timepoints to silence the same class of retrotransposons in insect evolution.

evolutionary biology↗

bioRxiv2023

Deformed wing virus genotypes A and B do not elicit immunologically different responses in naive honey bee hosts

Deformed wing virus (DWV), in association with Varroa destructor, is currently the leading factor associated with global honey bee deaths. With the exception of Australia, the virus and mite have a near global distribution, making it difficult to separate the effect of one from the other. Over time, the prevalence of the two main DWV genotypes (DWV-A and DWV-B) has changed, leading to the suggestion that the two strains elicit a different immune response by the host, the western honey bee Apis mellifera. Here we use a honey bee population naive to both the mite and the virus to investigate if honey bees show a different immunological response to DWV genotypes. We examined the expression of 19 immune genes by RT-qPCR and comprehensively analysed the small RNA response in honey bees after experimental injection with DWV-A and DWV-B. We found no evidence to indicate that DWV-A and DWV-B elicit a different immune response in honey bees. We found that RNA interference genes are up-regulated during DWV infection and that the small interfering RNA (siRNA) response is proportional to viral loads, yet does not inhibit the virus from accumulating to high loads. We also found that the siRNA response towards DWV was weaker than the response to another honey bee pathogen, Black queen cell virus. This suggests that DWV is comparatively better at evading antiviral host defences. There was no evidence for the production of virus-derived PIWI-RNAs in response to DWV infection. In contrast to previous studies, and in the absence of V. destructor, we found no evidence that DWV has an immunosuppressive effect in honey bees. Overall, our results advance our understanding of the immunological effect DWV elicits in honey bees.

immunology↗

bioRxiv2023

Virus replication in the honey bee parasite, Varroa destructor

Arthropod vectors such as mites and ticks introduce an alternative viral transmission route between their hosts. The ectoparasitic mite Varroa destructor is the leading threat to the health of Western honey bees (Apis mellifera) primarily through its action as a vector of viruses. However, it is unclear whether viruses transmitted by V. destructor actively infect and replicate in mites, which could facilitate increased transmission and select for more virulent strains. To better understand the role of V. destructor as a vector, we took advantage of differences between bee and mite antiviral RNA interference pathways to identify the host specificity of replicating viruses. We used small RNA sequencing of individual V. destructor mites to examine viral small interfering RNA (vsiRNA) profiles of Deformed wing virus genotypes (DWV-A and DWV-B), associated with colony declines, as well as nine other viruses present in our samples. We found active replication of six V. destructor-associated viruses, including a novel virus, Varroa destructor virus 9 (VDV-9), and replication of two honey bee associated viruses, including both DWV-A and -B genotypes, suggesting that mites are biological vectors for important bee pathogens. We show that the antiviral RNAi response can be used define the host range of viruses in host-parasite interactions, such as honey bees and their parasites, enabling a better understanding of the role of a vector in the evolution and spread of honey bee pathogens.

genetics↗

bioRxiv2021

Abundant small RNAs in the reproductive tissues of the honey bee, Apis mellifera, are a plausible mechanism for epigenetic inheritance and parental manipulation of gene expression

Polyandrous social insects such as the honey bee are prime candidates for parental manipulation of gene expression in offspring. Although there is good evidence for parent-of-origin effects in honey bees the epigenetic mechanisms that underlie these effects remain a mystery. Small RNA molecules such as miRNAs, piRNAs and siRNAs play important roles in transgenerational epigenetic inheritance and in the regulation of gene expression during development. Here we present the first characterisation of small RNAs present in honey bee reproductive tissues: ovaries, spermatheca, semen, fertilised and unfertilised eggs, and testes. We show that semen contains fewer piRNAs relative to eggs and ovaries, and that piRNAs and miRNAs which map antisense to genes involved in DNA regulation and developmental processes are differentially expressed between tissues. tRNA fragments are highly abundant in semen and have a similar profile to those seen in semen in other animals. Intriguingly we find abundant piRNAs that target the sex determination locus, suggesting that piRNAs may play a role in honey bee sex determination. We conclude that small RNAs play a fundamental role in honey bee gametogenesis and reproduction and provide a plausible mechanism for parent-of origin-effects on gene expression and reproductive physiology.

genomics↗

bioRxiv2018

The chromatin modifiers SET-25 and SET-32 are required for initiation but not long-term maintenance of transgenerational epigenetic inheritance

Some epigenetic modifications are inherited from one generation to the next, providing a potential mechanism for the inheritance of environmentally acquired traits. Transgenerational inheritance of RNA interference phenotypes in Caenorhabditis elegans provides an excellent model to study this phenomenon, and whilst studies have implicated both chromatin modifications and small RNA pathways in heritable silencing their relative contributions remain unclear. Here we demonstrate that the histone methyltransferases SET-25 and SET-32 are required for the establishment of a transgenerational silencing signal but not for long-term maintenance of this signal between subsequent generations, suggesting that transgenerational epigenetic inheritance is a multi-step process with distinct genetic requirements for establishment and maintenance of heritable silencing. Furthermore, small RNA sequencing reveals that the abundance of secondary siRNAs (thought to be the effector molecules of heritable silencing) does not correlate with silencing phenotypes. Together, our results suggest that the current mechanistic models of epigenetic inheritance are incomplete.

genetics↗