Biology subjects

Bryon, A.

Publications and source records attributed to Bryon, A..

3 recordsLinked to original sources

bioRxiv2025

Transcriptome mining reveals diversity and evolution of iflaviruses in Lepidoptera

Insects are associated with a wide variety of diverse RNA viruses, including iflaviruses, a group of positive stranded RNA viruses that mainly infect arthropods. Whereas some iflaviruses cause severe diseases in insects, numerous iflaviruses that were detected in healthy populations of butterflies and moths (order: Lepidoptera) do not show apparent symptoms. Compared to other hosts, only few iflavirus genomes for lepidopteran hosts could be found in publicly available databases and we know little about the occurrence of iflaviruses in natural and laboratory lepidopteran populations. To expand the known diversity of iflaviruses in Lepidoptera, we developed a pipeline to automatically reconstruct virus genomes from public transcriptome data. We reconstructed 1,548 virus genomes from 55 different lepidopteran species that we were identified as coding-complete based on their length. To include incompletely assembled genomes, we developed a reference-based patching approach, resulting in 240 patched genomes. By including publicly available genomes, we inferred a phylogeny consisting of 139 non-redundant iflavirus genomes. Of these, 65 represent novel complete genomes, of which 39 might even belong to novel virus species. Our analysis expanded virus host range, where highly similar viruses were found in the transcriptomes of different lepidopteran species, genera or even families. Additionally, we find two groups of lepidopteran species depending on the diversity of viruses that infect them: some species were only infected by closely related viruses, whereas other species are infected by highly diverse viruses from different regions of the phylogeny. Finally, we show that the evolution of one virus species, Iflavirus betaspexiguae, is impacted by recombination within the species, which is also supported by the co-occurrence of multiple strains within data sets. Our analysis demonstrates how data mining of publicly available sequencing data can be used at a large scale to reconstruct intra-family viral diversity which serves as a basis to study virus host range and evolution. Our results contain numerous novel viruses and novel virus-host associations, including viruses for relevant insect pests, highlighting the impact of iflaviruses in insect ecology and as potential biological control agents in the future.

genomics↗

bioRxiv2018

Long-term population studies uncover the genome structure and genetic basis of xenobiotic and host plant adaptation in the herbivore Tetranychus urticae

Pesticide resistance arises rapidly in arthropod herbivores, as can host plant adaptation, and both are significant problems in agriculture. These traits have been challenging to study as both are often polygenic and many arthropods are genetically intractable. Here, we examined the genetic architecture of pesticide resistance and host plant adaptation in the two-spotted spider mite, Tetranychus urticae, a global agricultural pest. We show that the short generation time and high fecundity of T. urticae can be readily exploited in experimental evolution designs for high-resolution mapping of quantitative traits. As revealed by selection with spirodiclofen, an acetyl-CoA decarboxylase inhibitor, in populations from a cross between a spirodiclofen resistant and a susceptible strain, and which also differed in performance on tomato, we found that a limited number of loci could explain quantitative resistance to this compound. These were resolved to narrow genomic intervals, suggesting specific candidate genes, including acetyl-CoA decarboxylase itself, clustered and copy variable cytochrome P450 genes, and NADPH cytochrome P450 reductase, which encodes a redox partner for cytochrome P450s. For performance on tomato, candidate genomic regions for response to selection were distinct from those responding to the synthetic compound and were consistent with a more polygenic architecture. In accomplishing this work, we exploited the continuous nature of allele frequency changes across experimental populations to resolve the existing fragmented T.urticae draft genome to pseudochromosomes. This improved assembly was indispensable for our analyses, as it will be for future research with this model herbivore that is exceptionally amenable to genetic studies.

genetics↗

bioRxiv2018

Genome-wide gene expression profiling reveals that cuticle alterations and P450 detoxification are associated with pyrethroid resistance in Anopheles arabiensis populations from Ethiopia

BACKGROUNDVector control is the main intervention in malaria control and elimination strategies. However, the development of insecticide resistance is one of the major challenges for controlling malaria vectors. Anopheles arabiensis populations in Ethiopia showed resistance against both DDT and the pyrethroid deltamethrin. Although a L1014F target-site resistance mutation was present in the voltage gated sodium channel of investigated populations, the levels of resistance and biochemical studies indicated the presence of additional resistance mechanisms. In this study, we used genome-wide transcriptome profiling by RNAseq to assess differentially expressed genes between three deltamethrin and DDT resistant An. arabiensis field populations (Tolay, Asendabo, Chewaka) and two susceptible strains (Sekoru and Mozambique).\n\nRESULTSBoth RNAseq analysis and RT-qPCR showed that a glutathione-S-transferase, gstd3, and a cytochrome P450 monooxygenase, cyp6p4, were significantly overexpressed in the group of resistant populations compared to the susceptible strains, suggesting that the enzymes they encode play a key role in metabolic resistance against deltamethrin or DDT. Furthermore, a gene ontology enrichment analysis showed that expression changes of cuticle related genes were strongly associated with insecticide resistance, although this did not translate in increased thickness of the procuticle.\n\nCONCLUSIONOur transcriptome sequencing of deltamethrin/DDT resistant An. arabiensis populations from Ethiopia suggests non-target site resistance mechanisms and pave the way for further investigation of the role of cuticle composition in resistance.

molecular biology↗