Benchmarking of virome metagenomic analysis approaches using a large, 60+ members, viral synthetic community

We report here efforts to benchmark performance of two widespread approaches for virome analysis, which target either virion-associated nucleic acids (VANA) or highly purified double-stranded RNAs (dsRNAs). This was achieved using synthetic communities of varying complexity levels, up to a highly co...

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Published in:Journal of virology Vol. 97; no. 11; p. e0130023
Main Authors: Schönegger, Deborah, Moubset, Oumaima, Margaria, Paolo, Menzel, Wulf, Winter, Stephan, Roumagnac, Philippe, Marais, Armelle, Candresse, Thierry
Format: Journal Article
Language:English
Published: United States 30.11.2023
Subjects:
DNA Viruses - classification
DNA Viruses - genetics
Metagenomics - methods
Metagenomics - standards
Plant Viruses - classification
Plant Viruses - genetics
RNA, Double-Stranded - genetics
Synthetic Biology - methods
Virion - genetics
Virome - genetics
Viruses - classification
Viruses - genetics
dsRNA
virome
high-thropughput sequencing
metagenome
VANA
synthetic community
double-stranded RNA
ISSN:1098-5514, 1098-5514
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Summary:We report here efforts to benchmark performance of two widespread approaches for virome analysis, which target either virion-associated nucleic acids (VANA) or highly purified double-stranded RNAs (dsRNAs). This was achieved using synthetic communities of varying complexity levels, up to a highly complex community of 72 viral agents (115 viral molecules) comprising isolates from 21 families and 61 genera of plant viruses. The results obtained confirm that the dsRNA-based approach provides a more complete representation of the RNA virome, in particular, for high complexity ones. However, for viromes of low to medium complexity, VANA appears a reasonable alternative and would be the preferred choice if analysis of DNA viruses is of importance. Several parameters impacting performance were identified as well as a direct relationship between the completeness of virome description and sample sequencing depth. The strategy, results, and tools used here should prove useful in a range of virome analysis efforts.
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ISSN:1098-5514
1098-5514
DOI:10.1128/jvi.01300-23