Computational methods for the discovery and annotation of viral integrations

Palatini, Umberto; Pischedda, Elisa; Bonizzoni, Mariangela

doi:10.1101/2021.08.28.458009

Cited by 2 publications

(3 citation statements)

References 44 publications

(60 reference statements)

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“…The third most abundant order, Bunyavirales (116 identified EVE integrations), is of interest due to its relative prevalence in several of these tick genomes. Though Bunyavirales-derived EVEs do appear in a multitude of arthropod genomes, they are often outnumbered by other viral orders [7,32]; in this analysis, they were identified in all nine tick genomes and were abundant in multiple species. Due to the fact that viral taxonomy within the order Bunyavirales is currently in flux (several of the viral top hits reported were only granted generic rank the prior year [38]), there may be additional EVEs derived from this lineage (and other viral orders) with even greater homology to loci identified herein that await discovery and/or classification.…”

Section: Resultsmentioning

confidence: 78%

“…There has yet to be a uniform methodology established for ensuring consistency in EVE results, both in regard to the steps taken to identify EVEs and the way individual EVEs identified as multiple BLAST HSPs should be classified (i.e., combined into one EVE or as several secondary EVEs), though more standardized approaches have recently been proposed [32]. In this analysis, discrete hits were treated as single EVEs where clear overlap occurred.…”

Section: Methodsmentioning

confidence: 99%

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Endogenous Viral Elements in Ixodid Tick Genomes

Barnes,

Price

2023

Viruses

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The documentation of endogenous viral elements (EVEs; virus-derived genetic material integrated into the genome of a nonviral host) has offered insights into how arthropods respond to viral infection via RNA interference pathways. Small non-coding RNAs derived from EVE loci serve to direct RNAi pathways in limiting replication and infection from cognate viruses, thus benefiting the host’s fitness and, potentially, vectorial capacity. Here we use informatic approaches to analyze nine available genome sequences of hard ticks (Acari: Ixodidae; Rhipicephalus sanguineus, R. microplus, R. annulatus, Ixodes ricinus, I. persulcatus, I. scapularis, Hyalomma asiaticum, Haemaphysalis longicornis, and Dermacentor silvarum) to identify endogenous viral elements and to illustrate the shared ancestry of all elements identified. Our results highlight a broad diversity of viral taxa as having given rise to 1234 identified EVEs in ticks, with Mononegavirales (specifically Rhabdoviridae) well-represented in this subset of hard ticks. Further investigation revealed extensive adintovirus integrations in several Ixodes species, the prevalence of Bunyavirales EVEs (notably not observed in mosquitoes), and the presence of several elements similar to known emerging human and veterinary pathogens. These results will inform subsequent work on current and past associations with tick species with regard to the viruses from which their “viral fossils” are derived and may serve as a reference for quality control of various tick-omics data that may suffer from misidentification of EVEs as viral genetic material.

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Section: Resultsmentioning

confidence: 78%

Section: Methodsmentioning

confidence: 99%

Endogenous Viral Elements in Ixodid Tick Genomes

Barnes,

Price

2023

Viruses

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“…The Vy-PER and ViR pipelines were run as previously described (32) to identify in the DNA of wild-collected mosquitoes nrEVEs which are absent in the AalbF2 assembly. Bioinformatic predictions of each of the newly identified viral integrations were molecularly confirmed by PCR using the DreamTaq Green PCR Master Mix 2X (Thermo Fisher) and nrEVE specific primers ( Table S3) .…”

Section: Methodsmentioning

confidence: 99%

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

Palatini

Alfano

Carballar-Lejarazú

et al. 2022

Preprint

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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.

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Computational methods for the discovery and annotation of viral integrations

Cited by 2 publications

References 44 publications

Endogenous Viral Elements in Ixodid Tick Genomes

Endogenous Viral Elements in Ixodid Tick Genomes

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

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