Revision of Begomovirus taxonomy based on pairwise sequence comparisons

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...

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Published in:	Archives of virology Vol. 160; no. 6; pp. 1593 - 1619
Main 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
Format:	Journal Article
Language:	English
Published:	Vienna Springer Vienna 01.06.2015 Springer Nature B.V
Subjects:	Begomovirus Begomovirus - classification Begomovirus - genetics Biomedical and Life Sciences Biomedicine Cloning Curtovirus DNA family Genetic engineering genome Genome, Viral - genetics Genomes genus Infectious Diseases Mastrevirus Medical Microbiology Pathogens Phylogeny Plant Diseases - virology Plants - virology Sequence Alignment species Taxonomy Virology Virology Division News Viruses Brazil Sequence Demarcation Tool Single-stranded DNA virus Taxonomy Whitefly-transmitted viruses Nomenclature Species demarcation
ISSN:	0304-8608, 1432-8798, 1432-8798
Online Access:	Get full text
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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.
AbstractList	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. 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. 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.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.
Author	Briddon, Rob W. Brown, Judith K. Zerbini, F. Murilo Moriones, Enrique Malathi, V. G. Ramos-Sobrinho, Roberto Varsani, Arvind Fiallo-Olivé, Elvira Idris, Ali Rivera-Bustamante, Rafael Martin, Darren P. Navas-Castillo, Jesús Silva, José C. F. Hernández-Zepeda, Cecilia Ueda, Shigenori
Author_xml	– sequence: 1 givenname: Judith K. surname: Brown fullname: Brown, Judith K. email: jbrown@ag.arizona.edu organization: School of Plant Sciences, University of Arizona – sequence: 2 givenname: F. Murilo surname: Zerbini fullname: Zerbini, F. Murilo email: zerbini@ufv.br organization: Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa – sequence: 3 givenname: Jesús surname: Navas-Castillo fullname: Navas-Castillo, Jesús organization: Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Instituto de Hortofruticultura Subtropical y Mediterránea, “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC) – sequence: 4 givenname: Enrique surname: Moriones fullname: Moriones, Enrique organization: Instituto de Hortofruticultura Subtropical y Mediterránea, “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC) – sequence: 5 givenname: Roberto surname: Ramos-Sobrinho fullname: Ramos-Sobrinho, Roberto organization: Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa – sequence: 6 givenname: José C. F. surname: Silva fullname: Silva, José C. F. organization: National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa – sequence: 7 givenname: Elvira surname: Fiallo-Olivé fullname: Fiallo-Olivé, Elvira organization: Dep. de Fitopatologia/BIOAGRO, Universidade Federal de Viçosa, National Research Institute for Plant-Pest Interactions (INCT-IPP), Universidade Federal de Viçosa, Instituto de Hortofruticultura Subtropical y Mediterránea, “La Mayora”, Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC) – sequence: 8 givenname: Rob W. surname: Briddon fullname: Briddon, Rob W. organization: National Institute for Biotechnology and Genetic Engineering – sequence: 9 givenname: Cecilia surname: Hernández-Zepeda fullname: Hernández-Zepeda, Cecilia organization: Centro de Investigación Científica de Yucatán, Unidad de Ciencias del Agua – sequence: 10 givenname: Ali surname: Idris fullname: Idris, Ali organization: Division of Biological and Environmental Sciences and Engineering, Center for Desert Agriculture, King Abdullah University of Science and Technology – sequence: 11 givenname: V. G. surname: Malathi fullname: Malathi, V. G. organization: Department of Plant Pathology, Adjunct Faculty, Tamil Nadu Agricultural University – sequence: 12 givenname: Darren P. surname: Martin fullname: Martin, Darren P. organization: Computational Biology Group, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town – sequence: 13 givenname: Rafael surname: Rivera-Bustamante fullname: Rivera-Bustamante, Rafael organization: Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav)-Unidad Irapuato – sequence: 14 givenname: Shigenori surname: Ueda fullname: Ueda, Shigenori organization: Kurume Research Station, National Agricultural Research, Center for Kyushu Okinawa Region – sequence: 15 givenname: Arvind surname: Varsani fullname: Varsani, Arvind organization: Electron Microscope Unit, University of Cape Town, Department of Plant Pathology and Emerging Pathogens Institute, University of Florida, School of Biological Sciences, University of Canterbury
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PMID	25894478
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PublicationCentury	2000
PublicationDate	2015-06-01
PublicationDateYYYYMMDD	2015-06-01
PublicationDate_xml	– month: 06 year: 2015 text: 2015-06-01 day: 01
PublicationDecade	2010
PublicationPlace	Vienna
PublicationPlace_xml	– name: Vienna – name: Austria – name: Wien
PublicationSubtitle	Official Journal of the Virology Division of the International Union of Microbiological Societies
PublicationTitle	Archives of virology
PublicationTitleAbbrev	Arch Virol
PublicationTitleAlternate	Arch Virol
PublicationYear	2015
Publisher	Springer Vienna Springer Nature B.V
Publisher_xml	– name: Springer Vienna – name: Springer Nature B.V
References	BrownJKFrohlichDRRosellRCThe sweetpotato or silverleaf whiteflies: biotypes of Bemisia tabaci or a species complex?Annu Rev Entomol19954051153410.1146/annurev.en.40.010195.0024551:CAS:528:DyaK2MXjtVWlt7g%3D CostaASBirdJMaramoroschKIncrease in the populational density of Bemisia tabaci, a threat to widespread virus infection of legume crops in BrazilTropical diseases of legumes1975New YorkAcademic Press171 Brown JK, Fauquet CM, Briddon RW, Zerbini FM, Moriones E, Navas-Castillo J (2012) Family Geminiviridae. In: King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ (eds) Virus taxonomy. Ninth report of the international committee on taxonomy of viruses. Elsevier Academic Press, London, pp 351–373 BrownJKBirdJWhitefly-transmitted geminiviruses and associated disorders in the Americas and the Caribbean basinPlant Dis19927622022510.1094/PD-76-0220 MelgarejoTAKonTRojasMRPaz-CarrascoLZerbiniFMGilbertsonRLCharacterization of a new world monopartite begomovirus causing leaf curl disease of tomato in Ecuador and Peru reveals a new direction in geminivirus evolutionJ Virol2013875397541310.1128/JVI.00234-1336481961:CAS:528:DC%2BC3sXnsV2lsrc%3D23468482 BernardoPGoldenMAkramMNaimuddinNadarajan NFernandezEGranierMRebeloAGPeterschmittMMartinDPRoumagnacPIdentification and characterisation of a highly divergent geminivirus: evolutionary and taxonomic implicationsVirus Res2013177354510.1016/j.virusres.2013.07.0061:CAS:528:DC%2BC3sXht1Gmu7zK23886668 NgTFFDuffySPolstonJEBixbyEValladGEBreitbartMExploring the diversity of plant DNA viruses and their satellites using vector-enabled metagenomics on whitefliesPLOS One20116e1905010.1371/journal.pone.001905030813221:CAS:528:DC%2BC3MXlsVantbo%3D21544196 MoralesFJJonesPGThe ecology and epidemiology of whitefly-transmitted viruses in Latin AmericaVirus Res2004100576510.1016/j.virusres.2003.12.0141:CAS:528:DC%2BD2cXht1yrsLs%3D15036836 HamiltonWDSteinVECouttsRHABuckKWComplete nucleotide sequence of the infectious cloned DNA components of tomato golden mosaic virus: potential coding regions and regulatory sequencesEMBO J19843219722055576661:CAS:528:DyaL2cXmt1eltL8%3D16453557 Van RegenmortelMHAckermannHWCalisherCHDietzgenRGHorzinekMCKeilGMMahyBWMartelliGPMurphyFAPringleCRimaBKSkernTVettenHJWeaverSCVirus species polemics: 14 senior virologists oppose a proposed change to the ICTV definition of virus speciesArch Virol20131581115111910.1007/s00705-012-1583-51:CAS:528:DC%2BC3sXmsFWqu78%3D23269443 OworBEShepherdDNTaylorNJEdemaRMonjaneALThomsonJAMartinDPVarsaniASuccessful application of FTA Classic Card technology and use of bacteriophage phi29 DNA polymerase for large-scale field sampling and cloning of complete maize streak virus genomesJ Virol Methods200714010010510.1016/j.jviromet.2006.11.0041:CAS:528:DC%2BD2sXhtlClsr0%3D17174409 EdwardsRARohwerFViral metagenomicsNat Rev Microbiol2005350451010.1038/nrmicro11631:CAS:528:DC%2BD2MXksFKmsLs%3D15886693 Sanchez-CamposSMartinez-AyalaAMarquez-MartinBAragon-CaballeroLNavas-CastilloJMorionesEFulfilling Koch’s postulates confirms the monopartite nature of tomato leaf deformation virus: a begomovirus native to the New WorldVirus Res201317328629310.1016/j.virusres.2013.02.0021:CAS:528:DC%2BC3sXjtl2jsb8%3D23415858 LoconsoleGSaldarelliPDoddapaneniHSavinoVMartelliGPSaponariMIdentification of a single-stranded DNA virus associated with citrus chlorotic dwarf disease, a new member in the family GeminiviridaeVirology201243216217210.1016/j.virol.2012.06.0051:CAS:528:DC%2BC38XpsVyjsrg%3D22749878 IdrisAAl-SalehMPiatekMJAl-ShahwanIAliSBrownJKViral metagenomics: analysis of begomoviruses by Illumina high-throughput sequencingViruses201461219123610.3390/v603121939701471:CAS:528:DC%2BC2MXjtlyitr4%3D24625811 ShepherdDNMartinDPLefeuvrePMonjaneALOworBERybickiEPVarsaniAA protocol for the rapid isolation of full geminivirus genomes from dried plant tissueJ Virol Methods20081499710210.1016/j.jviromet.2007.12.0141:CAS:528:DC%2BD1cXjtlehtr8%3D18280590 MorraMRPettyITDTissue specificity of geminivirus infection is genetically determinedPlant Cell2000122259227010.1105/tpc.12.11.22591501721:CAS:528:DC%2BD3MXos1Oj11090223 GilbertsonRLFariaJCAhlquistPMaxwellDPGenetic diversity in geminiviruses causing bean golden mosaic disease: the nucleotide sequence of the infectious cloned DNA components of a Brazilian isolate of bean golden mosaic geminivirusPhytopathology19938370971510.1094/Phyto-83-7091:CAS:528:DyaK2cXhsFGgsbs%3D De BarroPJLiuSSBoykinLMDinsdaleABBemisia tabaci: a statement of species statusAnnu Rev Entomol20115611910.1146/annurev-ento-112408-08550420690829 KrenzBThompsonJRFuchsMPerryKLComplete genome sequence of a new circular DNA virus from grapevineJ Virol201286771510.1128/JVI.00943-1234163041:CAS:528:DC%2BC38XhtVegtr%2FM22733880 StanleyJGayMRNucleotide sequence of cassava latent virus DNANature198330126026210.1038/301260a01:CAS:528:DyaL3sXosVarsA%3D%3D MuhireBMVarsaniAMartinDPSDT: a virus classification tool based on pairwise sequence alignment and identity calculationPLOS One20149e10827710.1371/journal.pone.0108277417812625259891 HaibleDKoberSJeskeHRolling circle amplification revolutionizes diagnosis and genomics of geminivirusesJ Virol Methods200613591610.1016/j.jviromet.2006.01.0171:CAS:528:DC%2BD28XltVeks70%3D16513183 TamuraKPetersonDPetersonNStecherGNeiMKumarSMEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methodsMol Biol Evol2011282731273910.1093/molbev/msr12132036261:CAS:528:DC%2BC3MXht1eiu73K21546353 PadidamMBeachyRNFauquetCMClassification and identification of geminiviruses using sequence comparisonsJ Gen Virol19957624926310.1099/0022-1317-76-2-2491:CAS:528:DyaK2MXjtl2jsLs%3D7844548 RosarioKDuffySBreitbartMA field guide to eukaryotic circular single-stranded DNA viruses: insights gained from metagenomicsArch Virol20121571851187110.1007/s00705-012-1391-y1:CAS:528:DC%2BC38XhsVWhu7nM22760663 FauquetCMBriddonRWBrownJKMorionesEStanleyJZerbiniFMZhouXGeminivirus strain demarcation and nomenclatureArch Virol200815378382110.1007/s00705-008-0037-61:CAS:528:DC%2BD1cXkvFagtLg%3D18256781 VarsaniAMartinDPNavas-CastilloJMorionesEHernandez-ZepedaCIdrisAZerbiniFMBrownJKRevisiting the classification of curtoviruses based on genome-wide pairwise identityArch Virol20141591873188210.1007/s00705-014-1982-x1:CAS:528:DC%2BC2cXhtlSms70%3D24463952 GillRBrownJKStanslyPANaranjoSESystematics of Bemisia and Bemisia relatives: can molecular techniques solve the Bemisia tabaci complex conundrum—a taxonomist’s viewpointBemisia: bionomics and management of a global pest2010DordrechtSpringer529 Inoue-NagataAKAlbuquerqueLCRochaWBNagataTA simple method for cloning the complete begomovirus genome using the bacteriophage phi29 DNA polymeraseJ Virol Methods200411620921110.1016/j.jviromet.2003.11.0151:CAS:528:DC%2BD2cXltV2nsw%3D%3D14738990 MuhireBMartinDPBrownJKNavas-CastilloJMorionesEZerbiniFMRivera-BustamanteRMalathiVGBriddonRWVarsaniAA genome-wide pairwise-identity-based proposal for the classification of viruses in the genus Mastrevirus (family Geminiviridae)Arch Virol20131581411142410.1007/s00705-012-1601-71:CAS:528:DC%2BC3sXosFKms7c%3D23340592 GilbertsonRLHidayatSHMartinezRTLeongSAFariaJCMoralesFJMaxwellDPDifferentiation of bean-infecting geminiviruses by nucleic acid hybridization probes and aspects of bean golden mosaic in BrazilPlant Dis19917533634210.1094/PD-75-03361:CAS:528:DyaK3MXlsFCmurw%3D ZhangWOlsonNHBakerTSFaulknerLAgbandje-McKennaMBoultonMIDaviesJWMcKennaRStructure of the Maize streak virus geminate particleVirology200127947147710.1006/viro.2000.07391:CAS:528:DC%2BD3MXnvFOhuw%3D%3D11162803 BrownJKStanslyPANaranjoSEPhylogenetic biology of the Bemisia tabaci sibling species groupBemisia: bionomics and management of a global pest2010DordrechtSpringer3167 CandresseTFillouxDMuhireBJulianCGalziSFortGBernardoPDaugroisJHFernandezEMartinDPVarsaniARoumagnacPAppearances can be deceptive: revealing a hidden viral infection with deep sequencing in a plant quarantine contextPLOS One20149e10294510.1371/journal.pone.0102945411136125061967 HarrisonBDAdvances in geminivirus researchAnnu Rev Phytopathol198523558210.1146/annurev.py.23.090185.0004151:CAS:528:DyaL28XltFWmsLc%3D VarsaniANavas-CastilloJMorionesEHernández-ZepedaCIdrisABrownJKZerbiniFMMartinDPEstablishment of three new genera in the family Geminiviridae: Becurtovirus, Eragrovirus and TurncurtovirusArch Virol20141592193220310.1007/s00705-014-2050-21:CAS:528:DC%2BC2cXkslGku7Y%3D24658781 AlbuquerqueLCInoue-NagataAKPinheiroBResendeROMorionesENavas-CastilloJGenetic diversity and recombination analysis of sweepoviruses from BrazilVirol J2012924110.1186/1743-422X-9-241348517823082767 Brown JK (2007) The Bemisia tabaci complex: genetic and phenotypic variability drives begomovirus spread and virus diversification. APSNet Featur. doi:10.1094/APSnetFeature-2007-0107 DuffySHolmesECMultiple introductions of the old world begomovirus Tomato yellow leaf curl virus into the new worldAppl Environ Microb2007737114711710.1128/AEM.01150-071:CAS:528:DC%2BD2sXhtlSksb7I RosarioKBreitbartMExploring the viral world through metagenomicsCurr Opin Virol2011128929710.1016/j.coviro.2011.06.0041:CAS:528:DC%2BC3MXhsFCrsLfE22440785 EdgarRCMUSCLE: a multiple sequence alignment method with reduced time and space complexityBMC Bioinform2004511910.1186/1471-2105-5-113 NakhlaMKMaxwellDPMartinezRTCarvalhoMGGilbertsonRLWidespread occurrence of eastern Mediterranean “strain” of tomato yellow leaf curl geminivirus in tomatoes in the Dominican RepublicPlant Dis19947892610.1094/PD-78-0926D A Varsani (2398_CR36) 2014; 159 RL Gilbertson (2398_CR19) 1993; 83 A Varsani (2398_CR13) 2014; 159 RC Edgar (2398_CR15) 2004; 5 B Muhire (2398_CR12) 2013; 158 J Stanley (2398_CR7) 1983; 301 TFF Ng (2398_CR38) 2011; 6 K Rosario (2398_CR42) 2011; 1 A Idris (2398_CR39) 2014; 6 2398_CR28 BE Owor (2398_CR30) 2007; 140 DN Shepherd (2398_CR32) 2008; 149 RA Edwards (2398_CR37) 2005; 3 JK Brown (2398_CR26) 1992; 76 MH Regenmortel Van (2398_CR11) 2013; 158 P Bernardo (2398_CR35) 2013; 177 JK Brown (2398_CR22) 1995; 40 K Tamura (2398_CR16) 2011; 28 2398_CR1 MR Morra (2398_CR21) 2000; 12 W Zhang (2398_CR6) 2001; 279 G Loconsole (2398_CR34) 2012; 432 T Candresse (2398_CR40) 2014; 9 K Rosario (2398_CR41) 2012; 157 R Gill (2398_CR25) 2010 S Sanchez-Campos (2398_CR2) 2013; 173 MK Nakhla (2398_CR4) 1994; 78 PJ Barro De (2398_CR23) 2011; 56 JK Brown (2398_CR24) 2010 D Haible (2398_CR29) 2006; 135 LC Albuquerque (2398_CR17) 2012; 9 BM Muhire (2398_CR14) 2014; 9 AK Inoue-Nagata (2398_CR31) 2004; 116 BD Harrison (2398_CR9) 1985; 23 AS Costa (2398_CR27) 1975 WD Hamilton (2398_CR8) 1984; 3 FJ Morales (2398_CR18) 2004; 100 B Krenz (2398_CR33) 2012; 86 TA Melgarejo (2398_CR3) 2013; 87 M Padidam (2398_CR10) 1995; 76 CM Fauquet (2398_CR43) 2008; 153 S Duffy (2398_CR5) 2007; 73 RL Gilbertson (2398_CR20) 1991; 75
References_xml	– reference: NakhlaMKMaxwellDPMartinezRTCarvalhoMGGilbertsonRLWidespread occurrence of eastern Mediterranean “strain” of tomato yellow leaf curl geminivirus in tomatoes in the Dominican RepublicPlant Dis19947892610.1094/PD-78-0926D – reference: Inoue-NagataAKAlbuquerqueLCRochaWBNagataTA simple method for cloning the complete begomovirus genome using the bacteriophage phi29 DNA polymeraseJ Virol Methods200411620921110.1016/j.jviromet.2003.11.0151:CAS:528:DC%2BD2cXltV2nsw%3D%3D14738990 – reference: FauquetCMBriddonRWBrownJKMorionesEStanleyJZerbiniFMZhouXGeminivirus strain demarcation and nomenclatureArch Virol200815378382110.1007/s00705-008-0037-61:CAS:528:DC%2BD1cXkvFagtLg%3D18256781 – reference: HaibleDKoberSJeskeHRolling circle amplification revolutionizes diagnosis and genomics of geminivirusesJ Virol Methods200613591610.1016/j.jviromet.2006.01.0171:CAS:528:DC%2BD28XltVeks70%3D16513183 – reference: Sanchez-CamposSMartinez-AyalaAMarquez-MartinBAragon-CaballeroLNavas-CastilloJMorionesEFulfilling Koch’s postulates confirms the monopartite nature of tomato leaf deformation virus: a begomovirus native to the New WorldVirus Res201317328629310.1016/j.virusres.2013.02.0021:CAS:528:DC%2BC3sXjtl2jsb8%3D23415858 – reference: HamiltonWDSteinVECouttsRHABuckKWComplete nucleotide sequence of the infectious cloned DNA components of tomato golden mosaic virus: potential coding regions and regulatory sequencesEMBO J19843219722055576661:CAS:528:DyaL2cXmt1eltL8%3D16453557 – reference: KrenzBThompsonJRFuchsMPerryKLComplete genome sequence of a new circular DNA virus from grapevineJ Virol201286771510.1128/JVI.00943-1234163041:CAS:528:DC%2BC38XhtVegtr%2FM22733880 – reference: BernardoPGoldenMAkramMNaimuddinNadarajan NFernandezEGranierMRebeloAGPeterschmittMMartinDPRoumagnacPIdentification and characterisation of a highly divergent geminivirus: evolutionary and taxonomic implicationsVirus Res2013177354510.1016/j.virusres.2013.07.0061:CAS:528:DC%2BC3sXht1Gmu7zK23886668 – reference: RosarioKDuffySBreitbartMA field guide to eukaryotic circular single-stranded DNA viruses: insights gained from metagenomicsArch Virol20121571851187110.1007/s00705-012-1391-y1:CAS:528:DC%2BC38XhsVWhu7nM22760663 – reference: MelgarejoTAKonTRojasMRPaz-CarrascoLZerbiniFMGilbertsonRLCharacterization of a new world monopartite begomovirus causing leaf curl disease of tomato in Ecuador and Peru reveals a new direction in geminivirus evolutionJ Virol2013875397541310.1128/JVI.00234-1336481961:CAS:528:DC%2BC3sXnsV2lsrc%3D23468482 – reference: GillRBrownJKStanslyPANaranjoSESystematics of Bemisia and Bemisia relatives: can molecular techniques solve the Bemisia tabaci complex conundrum—a taxonomist’s viewpointBemisia: bionomics and management of a global pest2010DordrechtSpringer529 – reference: CandresseTFillouxDMuhireBJulianCGalziSFortGBernardoPDaugroisJHFernandezEMartinDPVarsaniARoumagnacPAppearances can be deceptive: revealing a hidden viral infection with deep sequencing in a plant quarantine contextPLOS One20149e10294510.1371/journal.pone.0102945411136125061967 – reference: BrownJKStanslyPANaranjoSEPhylogenetic biology of the Bemisia tabaci sibling species groupBemisia: bionomics and management of a global pest2010DordrechtSpringer3167 – reference: AlbuquerqueLCInoue-NagataAKPinheiroBResendeROMorionesENavas-CastilloJGenetic diversity and recombination analysis of sweepoviruses from BrazilVirol J2012924110.1186/1743-422X-9-241348517823082767 – reference: ShepherdDNMartinDPLefeuvrePMonjaneALOworBERybickiEPVarsaniAA protocol for the rapid isolation of full geminivirus genomes from dried plant tissueJ Virol Methods20081499710210.1016/j.jviromet.2007.12.0141:CAS:528:DC%2BD1cXjtlehtr8%3D18280590 – reference: GilbertsonRLHidayatSHMartinezRTLeongSAFariaJCMoralesFJMaxwellDPDifferentiation of bean-infecting geminiviruses by nucleic acid hybridization probes and aspects of bean golden mosaic in BrazilPlant Dis19917533634210.1094/PD-75-03361:CAS:528:DyaK3MXlsFCmurw%3D – reference: DuffySHolmesECMultiple introductions of the old world begomovirus Tomato yellow leaf curl virus into the new worldAppl Environ Microb2007737114711710.1128/AEM.01150-071:CAS:528:DC%2BD2sXhtlSksb7I – reference: VarsaniANavas-CastilloJMorionesEHernández-ZepedaCIdrisABrownJKZerbiniFMMartinDPEstablishment of three new genera in the family Geminiviridae: Becurtovirus, Eragrovirus and TurncurtovirusArch Virol20141592193220310.1007/s00705-014-2050-21:CAS:528:DC%2BC2cXkslGku7Y%3D24658781 – reference: Brown JK, Fauquet CM, Briddon RW, Zerbini FM, Moriones E, Navas-Castillo J (2012) Family Geminiviridae. In: King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ (eds) Virus taxonomy. Ninth report of the international committee on taxonomy of viruses. Elsevier Academic Press, London, pp 351–373 – reference: ZhangWOlsonNHBakerTSFaulknerLAgbandje-McKennaMBoultonMIDaviesJWMcKennaRStructure of the Maize streak virus geminate particleVirology200127947147710.1006/viro.2000.07391:CAS:528:DC%2BD3MXnvFOhuw%3D%3D11162803 – reference: EdgarRCMUSCLE: a multiple sequence alignment method with reduced time and space complexityBMC Bioinform2004511910.1186/1471-2105-5-113 – reference: MuhireBMVarsaniAMartinDPSDT: a virus classification tool based on pairwise sequence alignment and identity calculationPLOS One20149e10827710.1371/journal.pone.0108277417812625259891 – reference: TamuraKPetersonDPetersonNStecherGNeiMKumarSMEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methodsMol Biol Evol2011282731273910.1093/molbev/msr12132036261:CAS:528:DC%2BC3MXht1eiu73K21546353 – reference: De BarroPJLiuSSBoykinLMDinsdaleABBemisia tabaci: a statement of species statusAnnu Rev Entomol20115611910.1146/annurev-ento-112408-08550420690829 – reference: HarrisonBDAdvances in geminivirus researchAnnu Rev Phytopathol198523558210.1146/annurev.py.23.090185.0004151:CAS:528:DyaL28XltFWmsLc%3D – reference: MorraMRPettyITDTissue specificity of geminivirus infection is genetically determinedPlant Cell2000122259227010.1105/tpc.12.11.22591501721:CAS:528:DC%2BD3MXos1Oj11090223 – reference: CostaASBirdJMaramoroschKIncrease in the populational density of Bemisia tabaci, a threat to widespread virus infection of legume crops in BrazilTropical diseases of legumes1975New YorkAcademic Press171 – reference: LoconsoleGSaldarelliPDoddapaneniHSavinoVMartelliGPSaponariMIdentification of a single-stranded DNA virus associated with citrus chlorotic dwarf disease, a new member in the family GeminiviridaeVirology201243216217210.1016/j.virol.2012.06.0051:CAS:528:DC%2BC38XpsVyjsrg%3D22749878 – reference: BrownJKBirdJWhitefly-transmitted geminiviruses and associated disorders in the Americas and the Caribbean basinPlant Dis19927622022510.1094/PD-76-0220 – reference: RosarioKBreitbartMExploring the viral world through metagenomicsCurr Opin Virol2011128929710.1016/j.coviro.2011.06.0041:CAS:528:DC%2BC3MXhsFCrsLfE22440785 – reference: NgTFFDuffySPolstonJEBixbyEValladGEBreitbartMExploring the diversity of plant DNA viruses and their satellites using vector-enabled metagenomics on whitefliesPLOS One20116e1905010.1371/journal.pone.001905030813221:CAS:528:DC%2BC3MXlsVantbo%3D21544196 – reference: GilbertsonRLFariaJCAhlquistPMaxwellDPGenetic diversity in geminiviruses causing bean golden mosaic disease: the nucleotide sequence of the infectious cloned DNA components of a Brazilian isolate of bean golden mosaic geminivirusPhytopathology19938370971510.1094/Phyto-83-7091:CAS:528:DyaK2cXhsFGgsbs%3D – reference: MuhireBMartinDPBrownJKNavas-CastilloJMorionesEZerbiniFMRivera-BustamanteRMalathiVGBriddonRWVarsaniAA genome-wide pairwise-identity-based proposal for the classification of viruses in the genus Mastrevirus (family Geminiviridae)Arch Virol20131581411142410.1007/s00705-012-1601-71:CAS:528:DC%2BC3sXosFKms7c%3D23340592 – reference: VarsaniAMartinDPNavas-CastilloJMorionesEHernandez-ZepedaCIdrisAZerbiniFMBrownJKRevisiting the classification of curtoviruses based on genome-wide pairwise identityArch Virol20141591873188210.1007/s00705-014-1982-x1:CAS:528:DC%2BC2cXhtlSms70%3D24463952 – reference: MoralesFJJonesPGThe ecology and epidemiology of whitefly-transmitted viruses in Latin AmericaVirus Res2004100576510.1016/j.virusres.2003.12.0141:CAS:528:DC%2BD2cXht1yrsLs%3D15036836 – reference: StanleyJGayMRNucleotide sequence of cassava latent virus DNANature198330126026210.1038/301260a01:CAS:528:DyaL3sXosVarsA%3D%3D – reference: IdrisAAl-SalehMPiatekMJAl-ShahwanIAliSBrownJKViral metagenomics: analysis of begomoviruses by Illumina high-throughput sequencingViruses201461219123610.3390/v603121939701471:CAS:528:DC%2BC2MXjtlyitr4%3D24625811 – reference: 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Snippet	Viruses of the genus Begomovirus (family Geminiviridae ) are emergent pathogens of crops throughout the tropical and subtropical regions of the world. By... Viruses of the genus Begomovirus (family Geminiviridae) are emergent pathogens of crops throughout the tropical and subtropical regions of the world. By virtue...
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SubjectTerms	Begomovirus Begomovirus - classification Begomovirus - genetics Biomedical and Life Sciences Biomedicine Cloning Curtovirus DNA family Genetic engineering genome Genome, Viral - genetics Genomes genus Infectious Diseases Mastrevirus Medical Microbiology Pathogens Phylogeny Plant Diseases - virology Plants - virology Sequence Alignment species Taxonomy Virology Virology Division News Viruses
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Title	Revision of Begomovirus taxonomy based on pairwise sequence comparisons
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