Skip to Main content Skip to Navigation
Journal articles

Sequence-based taxonomic framework for the classification of uncultured single-stranded DNA viruses of the family Genomoviridae

Abstract : With the advent of metagenomics approaches, a large diversity of known and unknown viruses has been identified in various types of environmental, plant, and animal samples. One such widespread virus group is the recently established family Genomoviridae which includes viruses with small (∼2-2.4 kb), circular ssDNA genomes encoding rolling-circle replication initiation proteins (Rep) and unique capsid proteins. Here, we propose a sequence-based taxonomic framework for classification of 121 new virus genomes within this family. Genomoviruses display ∼47% sequence diversity, which is very similar to that within the well-established and extensively studied family Geminiviridae (46% diversity). Based on our analysis, we establish a 78% genome-wide pairwise identity as a species demarcation threshold. Furthermore, using a Rep sequence phylogeny-based analysis coupled with the current knowledge on the classification of geminiviruses, we establish nine genera within the Genomoviridae family. These are Gemycircularvirus (n = 73), Gemyduguivirus (n = 1), Gemygorvirus (n = 9), Gemykibivirus (n = 29), Gemykolovirus (n = 3), Gemykrogvirus (n = 3), Gemykroznavirus (n = 1), Gemytondvirus (n = 1), Gemyvongvirus (n = 1). The presented taxonomic framework offers rational classification of genomoviruses based on the sequence information alone and sets an example for future classification of other groups of uncultured viruses discovered using metagenomics approaches.
Complete list of metadatas

Cited literature [71 references]  Display  Hide  Download

https://hal-pasteur.archives-ouvertes.fr/pasteur-01977359
Contributor : Floran Bidault <>
Submitted on : Thursday, January 10, 2019 - 4:54:50 PM
Last modification on : Wednesday, April 29, 2020 - 2:14:16 PM
Long-term archiving on: : Thursday, April 11, 2019 - 5:52:18 PM

Licence


Distributed under a Creative Commons Attribution - NonCommercial 4.0 International License

Identifiers

Collections

Citation

Arvind Varsani, Mart Krupovic. Sequence-based taxonomic framework for the classification of uncultured single-stranded DNA viruses of the family Genomoviridae. Virus Evolution, Oxford University Press, 2017, 3 (1), pp.vew037. ⟨10.1093/ve/vew037⟩. ⟨pasteur-01977359⟩

Share

Metrics

Record views

105

Files downloads

290