A genome-wide pairwise-identity-based proposal for the classification of viruses in the genus Mastrevirus (family Geminiviridae)

Abstract

Recent advances in the ease with which the genomes of small circular single-stranded DNA viruses can be amplified, cloned, and sequenced have greatly accelerated the rate at which full genome sequences of mastreviruses (family Geminiviridae, genus Mastrevirus) are being deposited in public sequence databases. Although guidelines currently exist for species-level classification of newly determined, complete mastrevirus genome sequences, these are difficult to apply to large sequence datasets and are permissive enough that, effectively, a high degree of leeway exists for the proposal of new species and strains.The lack of a standardised and rigorous method for testing whether a new genome sequence deserves such a classification is resulting in increasing numbers of questionable mastrevirus species proposals. Importantly, the recommended sequence alignment and pairwise identity calculation protocols of the current guidelines could easily be modified to make the classification of newly determined mastrevirus genome sequences significantly more objective. Here, we propose modified versions of these protocols that should substantially minimise the degree of classification inconsistency that is permissible under the current system. To facilitate the objective application of these guidelines for mastrevirus species demarcation, we additionally present a user-friendly computer program, SDT (species demarcation tool), for calculating and graphically 123Arch Virol (2013) 158:1411-1424 DOI 10.1007/s00705-012-1601 displaying pairwise genome identity scores. We apply SDT to the 939 full genome sequences of mastreviruses that were publically available in May 2012, and based on the distribution of pairwise identity scores yielded by our protocol, we propose mastrevirus species and strain demarcation thresholds of [78 % and [94 % identity, respectively.

Molecular characterization and field survey of Iranian potato virus X isolates

“…Both the full genome and cp dataset trees were midpoint rooted and braches with less than 60 % bootstrap support were collapsed. Nucleotide pairwise sequence identity was calculated using SDT v1.0 [18].…”

Incidence and characterization of Potato virus V infections in Iran

“…Fig. 4 Maximum likelihood phylogenetic analysis of the P1 genes of PVV isolates from around the world their pairwise nucleotide comparisons (calculated using Muhire et al [13])…”

“…2004) implemented in MEGA 5 [12]. Pairwise identities were calculated with pairwise deletion of gaps using SDT 1.0 [13]. Maximum likelihood phylogenetic analysis was carried out using PHYML 3.0 [14] with GTR?I?G4 (CP gene dataset) and GTR?G4 (P1 gene dataset) as the best substitution models selected by RDP4 [15], with 1,000 bootstrap replicates.…”

Establishment of three new genera in the family Geminiviridae: Becurtovirus, Eragrovirus and Turncurtovirus

“…Genome-wide pairwise identity analysis of the 29 available becurtovirus genomes (404 pairwise comparisons) using SDT v1.0 (with the MUSCLE alignment option; available for download from http://web. cbio.uct.ac.za/SDT [26]) revealed pairwise identity peaks between 76 and 79 %, between 88 and 93 %, and between 95 and 100 % and valleys between 80 and 87 % and between 93 and 95 % (Fig. 4).…”

“…The Geminiviridae Study Group of the International Committee on Taxonomy of Viruses (ICTV) has proposed various guidelines on how new geminivirus genome sequences should be taxonomically classified and named [6,12,13,26,36]. At the genus level, geminiviruses have been classified based on host range, insect vector, genome organisation and genome-wide pairwise sequence identities, and the Ninth Report of the ICTV [6] acknowledged the existence of four genera: Mastrevirus, Begomovirus, Curtovirus and Topocuvirus.…”