Diversity and comparative genomics of chimeric viruses in Sphagnum-dominated peatlands

Abstract : A new group of viruses carrying naturally chimeric single-stranded (ss) DNA genomes that encompass genes derived from eukaryotic ssRNA and ssDNA viruses has been recently identified by metagenomic studies. The host range, genomic diversity, and abundance of these chimeric viruses, referred to as cruciviruses, remain largely unknown. In this article, we assembled and analyzed thirty-seven new crucivirus genomes from twelve peat viromes, representing twenty-four distinct genome organizations, and nearly tripling the number of available genomes for this group. All genomes possess the two characteristic genes encoding for the conserved capsid protein (CP) and a replication protein. Additional ORFs were conserved only in nearly identical genomes with no detectable similarity to known genes. Two cruciviruses possess putative introns in their replication-associated genes. Sequence and phylogenetic analyses of the replication proteins revealed intra-gene chimerism in at least eight chimeric genomes. This highlights the large extent of horizontal gene transfer and recombination events in the evolution of ssDNA viruses, as previously suggested. Read mapping analysis revealed that members of the 'Cruciviridae' group are particularly prevalent in peat viromes. Sequences matching the CP ranged from 0.6 up to 10.9 percent in the twelve peat viromes. In contrast, from sixty-nine available viromes derived from other environments, only twenty-four contained cruciviruses, which on average accounted for merely 0.2 percent of sequences. Overall, this study provides new genome information and insights into the diversity of chimeric viruses, a necessary first step in progressing toward an accurate quantification and host range identification of these new viruses.
Type de document :
Article dans une revue
Virus Evolution, Oxford University Press, 2016, 2 (2), pp.vew025. 〈10.1093/ve/vew025〉
Liste complète des métadonnées

https://hal-pasteur.archives-ouvertes.fr/pasteur-01977372
Contributeur : Floran Bidault <>
Soumis le : jeudi 10 janvier 2019 - 16:55:07
Dernière modification le : jeudi 7 février 2019 - 14:44:33

Fichier

Licence


Distributed under a Creative Commons Paternité - Pas d'utilisation commerciale 4.0 International License

Identifiants

Citation

Achim Quaiser, Mart Krupovic, Alexis Dufresne, André-Jean Francez, Simon Roux. Diversity and comparative genomics of chimeric viruses in Sphagnum-dominated peatlands. Virus Evolution, Oxford University Press, 2016, 2 (2), pp.vew025. 〈10.1093/ve/vew025〉. 〈pasteur-01977372〉

Partager

Métriques

Consultations de la notice

5

Téléchargements de fichiers

2