Revisiting the classification of curtoviruses based on genome-wide pairwise identity

Arvind Varsani, Darren P. Martin, Jesús Navas-Castillo, Enrique Moriones, Cecilia Hernández-Zepeda, Ali Idris, F. Murilo Zerbini, Judith K Brown

Research output: Contribution to journalArticle

29 Citations (Scopus)

Abstract

Members of the genus Curtovirus (family Geminiviridae) are important pathogens of many wild and cultivated plant species. Until recently, relatively few full curtovirus genomes have been characterised. However, with the 19 full genome sequences now available in public databases, we revisit the proposed curtovirus species and strain classification criteria. Using pairwise identities coupled with phylogenetic evidence, revised species and strain demarcation guidelines have been instituted. Specifically, we have established 77% genome-wide pairwise identity as a species demarcation threshold and 94% genome-wide pairwise identity as a strain demarcation threshold. Hence, whereas curtovirus sequences with >77% genome-wide pairwise identity would be classified as belonging to the same species, those sharing >94% identity would be classified as belonging to the same strain. We provide step-by-step guidelines to facilitate the classification of newly discovered curtovirus full genome sequences and a set of defined criteria for naming new species and strains. The revision yields three curtovirus species: Beet curly top virus (BCTV), Spinach severe surly top virus (SpSCTV) and Horseradish curly top virus (HrCTV).

Original languageEnglish (US)
Pages (from-to)1873-1882
Number of pages10
JournalArchives of Virology
Volume159
Issue number7
DOIs
StatePublished - 2014

Fingerprint

Geminiviridae
Genome
Viruses
Armoracia
Guidelines
Beta vulgaris
Spinacia oleracea
Databases

ASJC Scopus subject areas

  • Virology

Cite this

Varsani, A., Martin, D. P., Navas-Castillo, J., Moriones, E., Hernández-Zepeda, C., Idris, A., ... Brown, J. K. (2014). Revisiting the classification of curtoviruses based on genome-wide pairwise identity. Archives of Virology, 159(7), 1873-1882. https://doi.org/10.1007/s00705-014-1982-x

Revisiting the classification of curtoviruses based on genome-wide pairwise identity. / Varsani, Arvind; Martin, Darren P.; Navas-Castillo, Jesús; Moriones, Enrique; Hernández-Zepeda, Cecilia; Idris, Ali; Murilo Zerbini, F.; Brown, Judith K.

In: Archives of Virology, Vol. 159, No. 7, 2014, p. 1873-1882.

Research output: Contribution to journalArticle

Varsani, A, Martin, DP, Navas-Castillo, J, Moriones, E, Hernández-Zepeda, C, Idris, A, Murilo Zerbini, F & Brown, JK 2014, 'Revisiting the classification of curtoviruses based on genome-wide pairwise identity', Archives of Virology, vol. 159, no. 7, pp. 1873-1882. https://doi.org/10.1007/s00705-014-1982-x
Varsani A, Martin DP, Navas-Castillo J, Moriones E, Hernández-Zepeda C, Idris A et al. Revisiting the classification of curtoviruses based on genome-wide pairwise identity. Archives of Virology. 2014;159(7):1873-1882. https://doi.org/10.1007/s00705-014-1982-x
Varsani, Arvind ; Martin, Darren P. ; Navas-Castillo, Jesús ; Moriones, Enrique ; Hernández-Zepeda, Cecilia ; Idris, Ali ; Murilo Zerbini, F. ; Brown, Judith K. / Revisiting the classification of curtoviruses based on genome-wide pairwise identity. In: Archives of Virology. 2014 ; Vol. 159, No. 7. pp. 1873-1882.
@article{9a3d3d4f881348909653a4d0121ba5c7,
title = "Revisiting the classification of curtoviruses based on genome-wide pairwise identity",
abstract = "Members of the genus Curtovirus (family Geminiviridae) are important pathogens of many wild and cultivated plant species. Until recently, relatively few full curtovirus genomes have been characterised. However, with the 19 full genome sequences now available in public databases, we revisit the proposed curtovirus species and strain classification criteria. Using pairwise identities coupled with phylogenetic evidence, revised species and strain demarcation guidelines have been instituted. Specifically, we have established 77{\%} genome-wide pairwise identity as a species demarcation threshold and 94{\%} genome-wide pairwise identity as a strain demarcation threshold. Hence, whereas curtovirus sequences with >77{\%} genome-wide pairwise identity would be classified as belonging to the same species, those sharing >94{\%} identity would be classified as belonging to the same strain. We provide step-by-step guidelines to facilitate the classification of newly discovered curtovirus full genome sequences and a set of defined criteria for naming new species and strains. The revision yields three curtovirus species: Beet curly top virus (BCTV), Spinach severe surly top virus (SpSCTV) and Horseradish curly top virus (HrCTV).",
author = "Arvind Varsani and Martin, {Darren P.} and Jes{\'u}s Navas-Castillo and Enrique Moriones and Cecilia Hern{\'a}ndez-Zepeda and Ali Idris and {Murilo Zerbini}, F. and Brown, {Judith K}",
year = "2014",
doi = "10.1007/s00705-014-1982-x",
language = "English (US)",
volume = "159",
pages = "1873--1882",
journal = "Archives of Virology",
issn = "0304-8608",
publisher = "Springer Wien",
number = "7",

}

TY - JOUR

T1 - Revisiting the classification of curtoviruses based on genome-wide pairwise identity

AU - Varsani, Arvind

AU - Martin, Darren P.

AU - Navas-Castillo, Jesús

AU - Moriones, Enrique

AU - Hernández-Zepeda, Cecilia

AU - Idris, Ali

AU - Murilo Zerbini, F.

AU - Brown, Judith K

PY - 2014

Y1 - 2014

N2 - Members of the genus Curtovirus (family Geminiviridae) are important pathogens of many wild and cultivated plant species. Until recently, relatively few full curtovirus genomes have been characterised. However, with the 19 full genome sequences now available in public databases, we revisit the proposed curtovirus species and strain classification criteria. Using pairwise identities coupled with phylogenetic evidence, revised species and strain demarcation guidelines have been instituted. Specifically, we have established 77% genome-wide pairwise identity as a species demarcation threshold and 94% genome-wide pairwise identity as a strain demarcation threshold. Hence, whereas curtovirus sequences with >77% genome-wide pairwise identity would be classified as belonging to the same species, those sharing >94% identity would be classified as belonging to the same strain. We provide step-by-step guidelines to facilitate the classification of newly discovered curtovirus full genome sequences and a set of defined criteria for naming new species and strains. The revision yields three curtovirus species: Beet curly top virus (BCTV), Spinach severe surly top virus (SpSCTV) and Horseradish curly top virus (HrCTV).

AB - Members of the genus Curtovirus (family Geminiviridae) are important pathogens of many wild and cultivated plant species. Until recently, relatively few full curtovirus genomes have been characterised. However, with the 19 full genome sequences now available in public databases, we revisit the proposed curtovirus species and strain classification criteria. Using pairwise identities coupled with phylogenetic evidence, revised species and strain demarcation guidelines have been instituted. Specifically, we have established 77% genome-wide pairwise identity as a species demarcation threshold and 94% genome-wide pairwise identity as a strain demarcation threshold. Hence, whereas curtovirus sequences with >77% genome-wide pairwise identity would be classified as belonging to the same species, those sharing >94% identity would be classified as belonging to the same strain. We provide step-by-step guidelines to facilitate the classification of newly discovered curtovirus full genome sequences and a set of defined criteria for naming new species and strains. The revision yields three curtovirus species: Beet curly top virus (BCTV), Spinach severe surly top virus (SpSCTV) and Horseradish curly top virus (HrCTV).

UR - http://www.scopus.com/inward/record.url?scp=84903595327&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84903595327&partnerID=8YFLogxK

U2 - 10.1007/s00705-014-1982-x

DO - 10.1007/s00705-014-1982-x

M3 - Article

C2 - 24463952

AN - SCOPUS:84903595327

VL - 159

SP - 1873

EP - 1882

JO - Archives of Virology

JF - Archives of Virology

SN - 0304-8608

IS - 7

ER -