Computational Methods for the Discovery and Annotation of Viral Integrations

Palatini, Umberto; Pischedda, Elisa; Bonizzoni, Mariangela

doi:10.1007/978-1-0716-2380-0_18

Cited by 4 publications

(1 citation statement)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The frequency of each of the 252 nrEVEs annotated in AaegL5 was established in each of the analyzed populations using the SVD pipeline (46,48,154). The same procedure was used to verify the occurrence of Ae.…”

Section: Analysis Of Ae Aegypti Nrevesmentioning

confidence: 99%

Molecular signature of domestication in the arboviral vectorAedes aegypti

Lozada-Chavez

Lozada-Chávez

Alfano

et al. 2023

Preprint

View full text Add to dashboard Cite

Background: Domestication is a complex, multi-stage and species-specific process that results in organisms living close to humans. In the arboviral vectorAedes aegyptiadaptation to living in proximity with anthropogenic environments has been recognized as a major evolutionary shift, separating a generalist form,Aedes aegypti formosus(Aaf), from the domestic formAedes aegypti aegypti(Aaa), which tends to deposit eggs artificial containers and bite humans for a blood meal. These behaviors enhance the mosquito vectorial capacity. The extent to which domestication has impacted theAe. aegyptigenome has not been thoroughly investigated yet. Results: Taking advantage of two forms' distinct and historically documented geographic distributions, we analyzed the genomes of 634 worldwideAe. aegyptimosquitoes. Using more than 300 million high-confidence SNPs, we found a unique origin for all out-of-AfricaAe. aegyptimosquitoes, with no evidence of admixture events in Africa, apart from Kenya. A group of 1033 genes were under positive selection only in out-of-Africa mosquitoes and 236 genes had nonsynonymous mutations, occurring at statistically different frequencies in Aaa and Aaf mosquitoes. Conclusion: We identified a clear signal of genetic differentiation between Aaa and Aaf, circumscribed to a catalogue of candidate genes. TheseAaa molecular signaturegenes extend beyond chemosensory genes to genes linked to neuronal and hormonal functions. This suggests that the behavioral shift to domestication may rely on the fine regulation of metabolic and neuronal functions, more than the role of a few significant genes. Our results also provide the foundation to investigate new targets for the control ofAe. aegyptipopulations.

show abstract

Section: Analysis Of Ae Aegypti Nrevesmentioning

confidence: 99%

Molecular signature of domestication in the arboviral vectorAedes aegypti

Lozada-Chavez

Lozada-Chávez

Alfano

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

Endogenous viral elements: insights into data availability and accessibility

Ritsch,

Brait,

Harvey

et al. 2024

Virus Evolution

View full text Add to dashboard Cite

Endogenous viral elements (EVEs) are remnants of viral genetic material endogenized into the host genome. They have, in the last decades, attracted attention for their role as potential contributors to pathogenesis, drivers of selective advantage for the host, and genomic remnants of ancient viruses. EVEs have a nuanced and complex influence on both host health and evolution, and can offer insights on the deep evolutionary history of viruses. As an emerging field of research, several factors limit a comprehensive understanding of EVEs: they are currently underestimated and periodically overlooked in studies of the host genome, transcriptome, and virome. The absence of standardized guidelines for ensuring EVE-related data availability and accessibility following the FAIR (‘findable, accessible, interoperable, and reusable’) principles obstructs our ability to gather and connect information. Here, we discuss challenges to the availability and accessibility of EVE-related data and propose potential solutions. We identified the biological and research focus imbalance between different types of EVEs, and their overall biological complexity as genomic loci with viral ancestry, as potential challenges that can be addressed with the development of a user-oriented identification tool. In addition, reports of EVE identification are scattered between different subfields under different keywords, and EVE sequences and associated data are not properly gathered in databases. While developing an open and dedicated database might be ideal, targeted improvements of generalist databases might provide a pragmatic solution to EVE data and metadata accessibility. The implementation of these solutions, as well as the collective effort by the EVE scientific community in discussing and setting guidelines, is now drastically needed to lead the development of EVE research and offer insights into host-virus interactions and their evolutionary history.

show abstract

Virome and nrEVEome diversity of Aedes albopictus mosquitoes from La Reunion Island and China

Palatini

Alfano

Carballar-Lejarazú

et al. 2022

Preprint

Self Cite

View full text Add to dashboard Cite

Background Aedes albopictus is a public health threat for its worldwide spread and ability to transmit arboviruses. Understanding mechanisms of mosquito immunity can provide new tools to control arbovirus spread. The genomes of Aedes mosquitoes contain hundreads of nonretroviral endogenous viral elements (nrEVEs), which are enriched in piRNA clusters and produce piRNAs, with the potential to target cognate viruses. Recently, one nrEVE was shown to limit cognate viral infection through nrEVE-derived piRNAs. These findings suggest that nrEVEs constitute an archive of past viral infection and that the landscape of viral integrations may be variable across populations depending on their viral exposure. Methods We used bioinformatics and molecular approaches to identify known and novel (i.e. absent in the reference genome) viral integrations in the genome of wild collected Aedes albopictus mosquitoes and characterize their virome. Results We showed that the landscape of viral integrations is dynamic with seven novel viral integrations being characterised, but does not correlate with the virome, which includes both viral species known and unknown to infect mosquitoes. However, the small RNA coverage profile of nrEVEs and the viral genomic contigs we identified confimed an interaction among these elements and the piRNA and siRNA pathways in mosquitoes. Conclusions Mosquitoes nrEVEs have been recently described as a new form of heritable, sequence-specific mechanism of antiviral immunity. Our results contribute to understanding the dynamic distribution of nrEVEs in the genomes of wild Ae. albopictus and their interaction with mosquito viruses.

show abstract

Computational Methods for the Discovery and Annotation of Viral Integrations

Cited by 4 publications

References 39 publications

Molecular signature of domestication in the arboviral vectorAedes aegypti

Molecular signature of domestication in the arboviral vectorAedes aegypti

Endogenous viral elements: insights into data availability and accessibility

Virome and nrEVEome diversity of Aedes albopictus mosquitoes from La Reunion Island and China

Contact Info

Product

Resources

About