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

Schönegger Deborah, Moubset Oumaima, Margaria Paolo, Menzel Wulf, Winter Stephan, Roumagnac Philippe, Marais Armelle, Candresse Thierry. 2023. Benchmarking of virome metagenomic analysis approaches using a large, 60+ members, viral synthetic community. Journal of Virology, 97 (11), 20 p.

https://doi.org/10.1128/jvi.01300-23

Article de revue ; Article de recherche ; Article de revue à facteur d'impact

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Url - jeu de données - Entrepôt autre : https://doi.org/10.57745/42WNRJ / Url - jeu de données - Entrepôt autre : https://doi.org/10.57745/T4UYPC

Liste HCERES des revues (en SHS) : oui

Thème(s) HCERES des revues (en SHS) : Psychologie-éthologie-ergonomie

Résumé : In contrast to microbial metagenomics, there has still been only limited efforts to benchmark performance of virome analysis approaches in terms of faithfulness to community structure and of completeness of virome description. While natural communities are more readily accessible, synthetic communities assembled using well-characterized isolates allow more accurate performance evaluation. Starting from authenticated, quality-controlled reference isolates from the DSMZ Plant Virus Collection, we have assembled synthetic communities of varying complexity up to a highly complex community of 72 viral agents (115 viral molecules) comprising isolates from 21 viral families and 61 genera. These communities were then analyzed using two approaches frequently used in ecology-oriented plant virus metagenomics: a virion-associated nucleic acids (VANA)-based strategy and a highly purified double-stranded RNAs (dsRNAs)-based one. The results obtained allowed to compare diagnostic sensitivity of these two approaches for groups of viruses and satellites with different genome types and confirmed that the dsRNA-based approach provides a more complete representation of the RNA virome. However, for viromes of low to medium complexity, VANA appears a reasonable alternative and would be the preferred choiceif analysis of DNA viruses is of importance. They also allowed to identify several important parameters and to propose hypotheses to explain differences in performance, in particular, differences in the imbalance in the representation of individual viruses using each approach. Remarkably, these analyses highlight a strong direct relationship between the completeness of virome description and sample sequencing depth which should prove useful in further virome analysis efforts.

Mots-clés Agrovoc : virus des végétaux, ARN satellite, virologie, écologie microbienne, virus bunchy top bananier, dsRNA viruses, indexage des virus des plantes, identification, séquence nucléotidique, phylogénie, virus