Revision of Begomovirus taxonomy based on pairwise sequence comparisons

Handle URI:
http://hdl.handle.net/10754/575648
Title:
Revision of Begomovirus taxonomy based on pairwise sequence comparisons
Authors:
Brown, Judith K.; Zerbini, F. Murilo; Navas-Castillo, Jesús; Moriones, Enrique; Ramos-Sobrinho, Roberto; Silva, José C. F.; Fiallo-Olivé, Elvira; Briddon, Rob W.; Hernández-Zepeda, Cecilia; Idris, Ali; Malathi, V. G.; Martin, Darren P.; Rivera-Bustamante, Rafael; Ueda, Shigenori; Varsani, Arvind
Abstract:
Viruses of the genus Begomovirus (family Geminiviridae) are emergent pathogens of crops throughout the tropical and subtropical regions of the world. By virtue of having a small DNA genome that is easily cloned, and due to the recent innovations in cloning and low-cost sequencing, there has been a dramatic increase in the number of available begomovirus genome sequences. Even so, most of the available sequences have been obtained from cultivated plants and are likely a small and phylogenetically unrepresentative sample of begomovirus diversity, a factor constraining taxonomic decisions such as the establishment of operationally useful species demarcation criteria. In addition, problems in assigning new viruses to established species have highlighted shortcomings in the previously recommended mechanism of species demarcation. Based on the analysis of 3,123 full-length begomovirus genome (or DNA-A component) sequences available in public databases as of December 2012, a set of revised guidelines for the classification and nomenclature of begomoviruses are proposed. The guidelines primarily consider a) genus-level biological characteristics and b) results obtained using a standardized classification tool, Sequence Demarcation Tool, which performs pairwise sequence alignments and identity calculations. These guidelines are consistent with the recently published recommendations for the genera Mastrevirus and Curtovirus of the family Geminiviridae. Genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomoviruses belonging to different species and strains, respectively. Procedures and guidelines are outlined for resolving conflicts that may arise when assigning species and strains to categories wherever the pairwise identity falls on or very near the demarcation threshold value.
KAUST Department:
Center for Desert Agriculture
Publisher:
Springer Nature
Journal:
Archives of Virology
Issue Date:
18-Apr-2015
DOI:
10.1007/s00705-015-2398-y
Type:
Article
ISSN:
0304-8608; 1432-8798
Sponsors:
The analysis described in this manuscript was part of the taxonomic proposal 2013.015a,bP, approved by the Executive Committee of the ICTV in July 2013 and ratified in March 2014. JKB and FMZ are past and current chairs, respectively, of the Geminiviridae Study Group of the ICTV. JNC, EM, RWB, CHZ, AI, VGM, DPM, RRB, SU and AV were members of the Geminiviridae SG during 2012-2014, when the work was performed. JNC and EM are members of the Research Group AGR-214, partially funded by Consejeria de Economia, Innovacion y Ciencia, Junta de Andalucia, Spain, cofinanced by FEDER-FSE. DPM and AV are supported by the National Research Foundation of South Africa.
Appears in Collections:
Articles; Center for Desert Agriculture; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.authorBrown, Judith K.en
dc.contributor.authorZerbini, F. Muriloen
dc.contributor.authorNavas-Castillo, Jesúsen
dc.contributor.authorMoriones, Enriqueen
dc.contributor.authorRamos-Sobrinho, Robertoen
dc.contributor.authorSilva, José C. F.en
dc.contributor.authorFiallo-Olivé, Elviraen
dc.contributor.authorBriddon, Rob W.en
dc.contributor.authorHernández-Zepeda, Ceciliaen
dc.contributor.authorIdris, Alien
dc.contributor.authorMalathi, V. G.en
dc.contributor.authorMartin, Darren P.en
dc.contributor.authorRivera-Bustamante, Rafaelen
dc.contributor.authorUeda, Shigenorien
dc.contributor.authorVarsani, Arvinden
dc.date.accessioned2015-08-24T08:34:59Zen
dc.date.available2015-08-24T08:34:59Zen
dc.date.issued2015-04-18en
dc.identifier.issn0304-8608en
dc.identifier.issn1432-8798en
dc.identifier.doi10.1007/s00705-015-2398-yen
dc.identifier.urihttp://hdl.handle.net/10754/575648en
dc.description.abstractViruses of the genus Begomovirus (family Geminiviridae) are emergent pathogens of crops throughout the tropical and subtropical regions of the world. By virtue of having a small DNA genome that is easily cloned, and due to the recent innovations in cloning and low-cost sequencing, there has been a dramatic increase in the number of available begomovirus genome sequences. Even so, most of the available sequences have been obtained from cultivated plants and are likely a small and phylogenetically unrepresentative sample of begomovirus diversity, a factor constraining taxonomic decisions such as the establishment of operationally useful species demarcation criteria. In addition, problems in assigning new viruses to established species have highlighted shortcomings in the previously recommended mechanism of species demarcation. Based on the analysis of 3,123 full-length begomovirus genome (or DNA-A component) sequences available in public databases as of December 2012, a set of revised guidelines for the classification and nomenclature of begomoviruses are proposed. The guidelines primarily consider a) genus-level biological characteristics and b) results obtained using a standardized classification tool, Sequence Demarcation Tool, which performs pairwise sequence alignments and identity calculations. These guidelines are consistent with the recently published recommendations for the genera Mastrevirus and Curtovirus of the family Geminiviridae. Genome-wide pairwise identities of 91 % and 94 % are proposed as the demarcation threshold for begomoviruses belonging to different species and strains, respectively. Procedures and guidelines are outlined for resolving conflicts that may arise when assigning species and strains to categories wherever the pairwise identity falls on or very near the demarcation threshold value.en
dc.description.sponsorshipThe analysis described in this manuscript was part of the taxonomic proposal 2013.015a,bP, approved by the Executive Committee of the ICTV in July 2013 and ratified in March 2014. JKB and FMZ are past and current chairs, respectively, of the Geminiviridae Study Group of the ICTV. JNC, EM, RWB, CHZ, AI, VGM, DPM, RRB, SU and AV were members of the Geminiviridae SG during 2012-2014, when the work was performed. JNC and EM are members of the Research Group AGR-214, partially funded by Consejeria de Economia, Innovacion y Ciencia, Junta de Andalucia, Spain, cofinanced by FEDER-FSE. DPM and AV are supported by the National Research Foundation of South Africa.en
dc.publisherSpringer Natureen
dc.titleRevision of Begomovirus taxonomy based on pairwise sequence comparisonsen
dc.typeArticleen
dc.contributor.departmentCenter for Desert Agricultureen
dc.identifier.journalArchives of Virologyen
dc.contributor.institutionUniv Arizona, Sch Plant Sci, Tucson, AZ 85721 USAen
dc.contributor.institutionUniv Fed Vicosa, Dept Fitopatol, BIOAGRO, BR-36570900 Vicosa, MG, Brazilen
dc.contributor.institutionUniv Fed Vicosa, Natl Res Inst Plant Pest Interact INCT IPP, BR-36570900 Vicosa, MG, Brazilen
dc.contributor.institutionUniv Malaga, Consejo Super Invest Cient IHSM UMA CSIC, Inst Hortofruticultura Subtrop & Mediterranea, Malaga 29750, Spainen
dc.contributor.institutionNatl Inst Biotechnol & Genet Engn, Faisalabad, Pakistanen
dc.contributor.institutionCtr Invest Cient Yucatan, Unidad Ciencias Agua, Cancun, Quintana Roo, Mexicoen
dc.contributor.institutionTamil Nadu Agr Univ, Adjunct Fac, Dept Plant Pathol, Coimbatore 641003, Tamil Nadu, Indiaen
dc.contributor.institutionUniv Cape Town, Inst Infect Dis & Mol Med, Computat Biol Grp, ZA-7925 Cape Town, South Africaen
dc.contributor.institutionGenet Ctr Invest Estudios Avanzados IPN Cinvestav, Dept Ingn Genet, Unidad Irapuato, Irapuato 36821, Gto, Mexicoen
dc.contributor.institutionCtr Kyushu Okinawa Reg, Kurume Res Stn, Natl Agr Res, Kurume, Fukuoka 8398503, Japanen
dc.contributor.institutionUniv Cape Town, Electron Microscope Unit, ZA-7701 Cape Town, South Africaen
dc.contributor.institutionUniv Florida, Dept Plant Pathol, Gainesville, FL 32611 USAen
dc.contributor.institutionUniv Florida, Emerging Pathogens Inst, Gainesville, FL 32611 USAen
dc.contributor.institutionUniv Canterbury, Sch Biol Sci, Christchurch 8140, New Zealanden
kaust.authorIdris, Alien
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