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.

Erratum to: Discovery of two small circular ssDNA viruses associated with the whitefly Bemisia tabaci

“…Even though the biology of these viruses remains elusive, they were recently described in association with a number of different organisms and environmental samples [3], and classified in nine genera [9]. In the present study, the VEM approach was used to discover novel small circular DNA viruses associated with B. tabaci whiteflies.…”

“…ORF2 has 1,029 nt with a 113 nt-long intron, and encodes a 342 aa putative Rep protein similar to RepA from pteropus associated gemycircularvirus 3 (KT732797, 99% coverage, 83% identity, e-value 0.0). The predicted aa sequence coded by this ORF also presented all characteristic genomoviridae aa motifs [9]: motif I (LVTYSQ), motif II (LHLHV), GRS domain (DILDVDGRHANVEPSA), motif III (YAIK), Walker A (GGTRTGKT), Walker B (VFDDI), and motif C (WVCN). Phylogenetic analysis of Rep deduced amino acids from the two new viruses was performed after alignment with representative genomovirus sequences (Fig.…”

“…Genomoviruses are single-stranded small circular DNA viruses from the family Genomoviridae [3,9]. Even though the biology of these viruses remains elusive, they were recently described in association with a number of different organisms and environmental samples [3], and classified in nine genera [9].…”

“…The antisense ORF is 1,664 nt-long, with a putative intron of 201 nt, sharing 75% aa identity with the Rep from dragonfly associated gemyduguivirus 1 (YP_009021852, 100% coverage, 4e-180). All typical genomoviridae aa motifs [9] were identified in the predicted aa sequence of this ORF: motif I (LLTYAQ), motif II (THYHA), GRS domain (RVFDIDSYHPNIL-RGI), motif III (YATK), Walker A (GPSRTGKT), Walker B (IFDDM), and motif C (WCNN). Sanger sequencing of three cloned plasmids confirmed the size and sequence of the NGS-derived genome, except for two nucleotide substitutions in one of the sequences.…”

“…Sanger sequencing of three cloned plasmids confirmed the size and sequence of the NGS-derived genome, except for two nucleotide substitutions in one of the sequences. The low genetic identity of the full genome of AdDF to other genomoviruses suggests that it is potentially classified as a new species within Genomoviridae [3,9].…”