Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes

Veglia, Alex J.; Bistolas, Kalia S. I.; Correa, Adrienne S.; Thurber, Rebecca Vega

doi:10.1101/2022.04.11.487905

Cited by 5 publications

(4 citation statements)

References 101 publications

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“…Dinoflagellate‐infecting RNA viruses (dinoRNAVs) are positive‐sense, single‐stranded RNA viruses hypothesized to infect the dinoflagellate symbionts (Family Symbiodiniaceae) that live in the tissues of reef‐building stony corals (Correa et al., 2013; Grupstra et al., 2022; Veglia et al., 2022). Although dinoRNAVs can be prevalent in coral colonies (Grupstra et al., 2022; Howe‐Kerr et al., 2023; Montalvo‐Proaño et al., 2017; Veglia et al., 2022), it is unclear how dinoRNAVs (or Symbiodiniaceae infected by dinoRNAVs) are transmitted among colonies. Recent work has shown that corallivorous (coral‐eating) fishes disperse 100 s of millions of live Symbiodiniaceae cells across reefscapes in their faeces each day (Grupstra et al., 2021).…”

Section: Applying Vampirus To Study a Novel Environmental Rna Virus D...mentioning

confidence: 99%

vAMPirus: A versatile amplicon processing and analysis program for studying viruses

Veglia,

Rivera‐Vicéns,

Grupstra

et al. 2024

Molecular Ecology Resources

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Amplicon sequencing is an effective and increasingly applied method for studying viral communities in the environment. Here, we present vAMPirus, a user‐friendly, comprehensive, and versatile DNA and RNA virus amplicon sequence analysis program, designed to support investigators in exploring virus amplicon sequencing data and running informed, reproducible analyses. vAMPirus intakes raw virus amplicon libraries and, by default, performs nucleotide‐ and amino acid‐based analyses to produce results such as sequence abundance information, taxonomic classifications, phylogenies and community diversity metrics. The vAMPirus analytical framework leverages 16 different opensource tools and provides optional approaches that can increase the ratio of biological signal‐to‐noise and thereby reveal patterns that would have otherwise been masked. Here, we validate the vAMPirus analytical framework and illustrate its implementation as a general virus amplicon sequencing workflow by recapitulating findings from two previously published double‐stranded DNA virus datasets. As a case study, we also apply the program to explore the diversity and distribution of a coral reef‐associated RNA virus. vAMPirus is streamlined within Nextflow, offering straightforward scalability, standardization and communication of virus lineage‐specific analyses. The vAMPirus framework is designed to be adaptable; community‐driven analytical standards will continue to be incorporated as the field advances. vAMPirus supports researchers in revealing patterns of virus diversity and population dynamics in nature, while promoting study reproducibility and comparability.

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Section: Applying Vampirus To Study a Novel Environmental Rna Virus D...mentioning

confidence: 99%

vAMPirus: A versatile amplicon processing and analysis program for studying viruses

Veglia,

Rivera‐Vicéns,

Grupstra

et al. 2024

Molecular Ecology Resources

Self Cite

View full text Add to dashboard Cite

show abstract

“…Dinoflagellate-infecting RNA viruses (dinoRNAVs) are positive-sense, single-stranded RNA viruses hypothesized to infect the dinoflagellate symbionts (Family Symbiodiniaceae) that live in the tissues of reef-building stony corals (Correa et al, 2013;Veglia et al, 2022). Although dinoRNAVs can be prevalent in coral colonies Howe-Kerr et al, 2022;Montalvo-Proaño et al, 2017;Veglia et al, 2022), it is unclear how dinoRNAVs (or Symbiodiniaceae infected by dinoRNAVs) are transmitted among colonies. Recent work has shown that corallivorous (coral-eating) fishes disperse 100s of millions of live Symbiodiniaceae cells across reefscapes in their feces each day (Grupstra et al, 2021).…”

Section: Rna Virus Study Descriptionmentioning

confidence: 99%

vAMPirus: A versatile amplicon processing and analysis program for studying viruses

Veglia

Rivera‐Vicéns

Grupstra

et al. 2023

Preprint

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Amplicon sequencing is an effective and increasingly applied method for studying viral communities in the environment. Here, we present vAMPirus, a user-friendly, comprehensive, and versatile DNA and RNA virus amplicon sequence analysis program, designed to support investigators in exploring virus amplicon sequencing data and running informed, reproducible analyses. vAMPirus intakes raw virus amplicon libraries and, by default, performs nucleotide- and protein-based analyses to produce results such as sequence abundance information, taxonomic classifications, phylogenies, and community diversity metrics. The vAMPirus pipelines additionally include optional approaches that can increase the biological signal-to-noise ratio in results by leveraging tools not yet commonly applied to virus amplicon data analyses. In this paper, we validate the vAMPirus analytical framework and illustrate its implementation into the general virus amplicon sequencing workflow by recapitulating findings from two previously published double-stranded DNA virus datasets. As a case study, we also apply the program to explore the diversity and distribution of a coral reef-associated RNA virus. vAMPirus is incorporated with the Nextflow workflow manager, offering straightforward scalability, standardization, and communication of virus lineage-specific analyses. The vAMPirus framework itself is also designed to be adaptable; community-driven analytical standards will continue to be incorporated as the field advances. vAMPirus supports researchers in revealing patterns of virus diversity and population dynamics in nature, while promoting study reproducibility and comparability.

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“…Overall, it was challenging to determine whether the identified transcripts stemmed from genomes of independent viruses or from integrated virus sequences within the host's genome since the study was based solely on RNA-Seq data. It is well-known that endogenous viral elements (EVEs) of DNA and non-retroviral RNA viruses are widespread across invertebrate genomes and these EVEs can be transcriptionally active (ter Horst et al, 2019;Veglia et al, 2023). Furthermore, EVEs of invertebrate genomes originate from a wider range of viral families when compared to vertebrate genomes and the abundance and diversity of EVEs is highly variable even between closely related invertebrate species (Gilbert & Belliardo, 2022).…”

Section: Read Taxonomic Classification Into Viral Familiesmentioning

confidence: 99%

Unveiling the Hidden Viromes Across the Animal Tree of Life: Insights from a Taxonomic Classification Pipeline Applied to Invertebrates of 31 Metazoan Phyla

Alfonso,

Butković,

Fernández

et al. 2023

Preprint

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Invertebrates constitute the majority of animal species on Earth, including most disease-causing agents or vectors, with more diverse viromes when compared to vertebrates. Recent advancements in high-throughput sequencing have significantly expanded our understanding of invertebrate viruses, yet this knowledge remains biased toward a few well-studied animal lineages. In this study, we analyze invertebrate DNA and RNA viromes for 31 phyla using 417 publicly available RNA-Seq datasets from diverse environments in the marine-terrestrial and marine-freshwater gradients. This study aims to (i) estimate virome compositions at the family level for the first time across the Animal Tree of Life, including the first exploration of the virome in several phyla, (ii) quantify the diversity of invertebrate viromes and characterize the structure of invertebrate-virus interaction networks, and (iii) investigate host phylum and habitat influence on virome differences. Results showed that a set of few viral families of eukaryotes, comprisingRetroviridae,Flaviviridaeand several families of giant DNA viruses, were ubiquitous and highly abundant. Nevertheless, some differences emerged between phyla, revealing for instance a less diverse virome in Ctenophora compared to the other animal phyla. Compositional analysis of the viromes showed that the host phylum explained over five times more variance in composition than its habitat. Moreover, significant similarities were observed between the viromes of some phylogenetically related phyla, which could highlight the influence of co-evolution in shaping invertebrate viromes.ImportanceThis study significantly enhances our understanding of the global animal virome by characterizing the viromes of previously unexamined invertebrate lineages from a large number of animal phyla. It showcases the great diversity of viromes within each phylum and investigates the role of habitat shaping animal viral communities. Furthermore, our research identifies dominant virus families in invertebrates and distinguishes phyla with analogous viromes. This study sets the road towards a deeper understanding of the virome across the Animal Tree of Life.

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Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes

Cited by 5 publications

References 101 publications

vAMPirus: A versatile amplicon processing and analysis program for studying viruses

vAMPirus: A versatile amplicon processing and analysis program for studying viruses

vAMPirus: A versatile amplicon processing and analysis program for studying viruses

Unveiling the Hidden Viromes Across the Animal Tree of Life: Insights from a Taxonomic Classification Pipeline Applied to Invertebrates of 31 Metazoan Phyla

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