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Publication Details
AFRICAN RESEARCH NEXUS
SHINING A SPOTLIGHT ON AFRICAN RESEARCH
immunology and microbiology
A genome-wide pairwise-identity-based proposal for the classification of viruses in the genus Mastrevirus (family Geminiviridae)
Archives of Virology, Volume 158, No. 6, Year 2013
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Description
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 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. © 2013 Springer-Verlag Wien.
Authors & Co-Authors
Muhire, Brejnev Muhizi
South Africa, Cape Town
University of Cape Town
Martin, Darren Patrick
South Africa, Cape Town
University of Cape Town
Brown, Judith K.
United States, Tucson
The University of Arizona
Navas-Castillo, Jesús
Spain, Malaga
Csic-uma - Instituto de Hortofruticultura Subtropical y Mediterranea la Mayora Ihsm
Moriones, E.
Spain, Malaga
Csic-uma - Instituto de Hortofruticultura Subtropical y Mediterranea la Mayora Ihsm
Zerbini, Francisco Murilo
Brazil, Vicosa
Universidade Federal de Vicosa
Rivera-Bustamante, R. F.
Mexico, Irapuato
Centro de Investigacion y de Estudio Avanzados, Campus Guanajuato
Malathi, Varagur Ganesan
India, New Delhi
Icar - Indian Agricultural Research Institute, new Delhi
Briddon, Rob William
Pakistan, Faisalabad
National Institute for Biotechnology and Genetic Engineering Pakistan
Varsani, Arvind
South Africa, Cape Town
University of Cape Town
New Zealand, Christchurch
University of Canterbury
Statistics
Citations: 235
Authors: 10
Affiliations: 8
Identifiers
Doi:
10.1007/s00705-012-1601-7
ISSN:
03048608
Research Areas
Genetics And Genomics