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Evidence that Cymbidium mosaic virus (CymMV) isolates divide into two subgroups based on nucleotide diversity of coat protein and replicase genes

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Summary

The genetic diversity of Cymbidium mosaic virus (CymMV, family Flexiviridae) was assessed by analysing the nucleotide sequences of coat protein (CP) and partial RNA-dependent RNA polymerase (RdRp) genes. Thirty CymMV sequences from vanilla isolates, obtained in this work by direct sequencing of RT-PCR products, were compared to the sequences from ornamental orchid isolates available in GenBank. The CymMV population exhibited overall low genetic diversity (π = 0.054 and π = 0.053 for CP and RdRp genes, respectively). Phylogenetic analyses of the 85 CP and 37 RdRp sequences revealed the segregation of the isolates into two congruent monophyletic clusters; however these two subgroups did not cluster in amino sequence analysis because most of the nt mutations were synonymous. Nevertheless, the subgrouping was confirmed by highly significant Kst tests for the CP and RdRp genes. Analysis of population genetic parameters and distribution of synonymous and nonsynonymous mutations revealed that both genes were under negative selection with no recombination events. These results suggested that the CymMV isolates found in cultivated orchids worldwide have a dual origin and are expanding as if following bottlenecks.

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References

  • MJ Adams JF Antoniw (2003) ArticleTitleCodon usage bias amongst plant viruses Arch Virol 149 113–135 Occurrence Handle14689279 Occurrence Handle10.1007/s00705-003-0186-6

    Article  PubMed  Google Scholar 

  • MJ Adams JF Antoniw M Bar-Joseph AA Brunt T Candresse GD Foster GP Martelli RG Milne SK Zavriev CM Fauquet (2004) ArticleTitleThe new plant virus family Flexiviridae and assessment of molecular criteria for species demarcation Arch Virol 149 1045–1460 Occurrence Handle15098118 Occurrence Handle1:CAS:528:DC%2BD2cXjt1Sgtr4%3D

    PubMed  CAS  Google Scholar 

  • PA Ajjikuttira CL Lim-Ho MH Woon RH Ryu CA Chang CS Loh SM Wong (2002) ArticleTitleGenetic variability in the coat protein genes of two orchid viruses: Cymbidium mosaic virus and Odontoglossum ringspot virus Arch Virol 147 1943–1954 Occurrence Handle12376755 Occurrence Handle10.1007/s00705-002-0868-5 Occurrence Handle1:CAS:528:DC%2BD38XnslaqtL8%3D

    Article  PubMed  CAS  Google Scholar 

  • J Albouy J-C Devergne (1998) Maladies à virus des plantes ornementales INRA Paris

    Google Scholar 

  • B Callaghan RG Dietzgen (2005) ArticleTitleNucleocapsid gene variability reveals two subgroups of Lettuce necrotic yellows virus Arch Virol 150 1661–1667 Occurrence Handle15824884 Occurrence Handle10.1007/s00705-005-0528-7 Occurrence Handle1:CAS:528:DC%2BD2MXmtlSqurk%3D

    Article  PubMed  CAS  Google Scholar 

  • ER Chare EC Holmes (2004) ArticleTitleSelection pressures in the capsid genes of plant RNA viruses reflect mode of transmission J Gen Virol 85 3149–3157 Occurrence Handle15448378 Occurrence Handle10.1099/vir.0.80134-0 Occurrence Handle1:CAS:528:DC%2BD2cXosV2gt7c%3D

    Article  PubMed  CAS  Google Scholar 

  • ER Chare EC Holmes (2006) ArticleTitleA phylogenetic survey of recombination frequency in plant RNA viruses Arch Virol 151 933–946 Occurrence Handle16292597 Occurrence Handle10.1007/s00705-005-0675-x Occurrence Handle1:CAS:528:DC%2BD28Xjs1Klurw%3D

    Article  PubMed  CAS  Google Scholar 

  • AJC Eun SM Wong (1999) ArticleTitleDetection of Cymbidium mosaic potexvirus and Odontoglossum ringspot tobamovirus using immuno-capillary zone electrophoresis Phytopathology 89 522–528 Occurrence Handle1:CAS:528:DyaK1MXjslyjsbc%3D

    CAS  Google Scholar 

  • AJC Eun L Huang FT Chew SFY Li SM Wong (2002) ArticleTitleDetection of two orchid viruses using quartz crystal microbalance-based DNA biosensors Phytopathology 92 654–658

    Google Scholar 

  • Fauquet C, Mayo MA, Maniloff J, Desselberger U, Ball LA (2005) Virus taxonomy. In: IUMS VD (ed) Elsevier, Academic Press, London, UK, pp 1259

  • YX Fu WH Li (1993) ArticleTitleStatistical tests of neutrality of mutations Genetics 133 693–709 Occurrence Handle8454210 Occurrence Handle1:STN:280:ByyB3c3kvVU%3D

    PubMed  CAS  Google Scholar 

  • A Gibbs A Mackenzie A Blanchfield P Cross C Wilson E Kitajima M Nightingale M Clements (2000) ArticleTitleViruses of orchids in Australia: their identification, biology and control Austral Orchid Rev 65 10–21

    Google Scholar 

  • S Gourdel F Leclerc-Le Quillec (2001) ArticleTitleCoat protein gene of Cymbidium mosaic virus from Vanilla fragrans in Reunion Island J Phytopathol 149 561–564 Occurrence Handle10.1046/j.1439-0434.2001.00633.x Occurrence Handle1:CAS:528:DC%2BD3MXnslKntLY%3D

    Article  CAS  Google Scholar 

  • M Grisoni F Davidson C Hyrondelle K Farreyrol ML Caruana M Pearson (2004) ArticleTitleNature, incidence and symptomatology of viruses infecting Vanilla tahitensis in French Polynesia Plant Dis 88 119–124

    Google Scholar 

  • TA Hall (1999) ArticleTitleBioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT Nucleic Acids Symposium Series 41 95–98 Occurrence Handle1:CAS:528:DC%2BD3cXhtVyjs7Y%3D

    CAS  Google Scholar 

  • EC Holmes (2003) ArticleTitleError thresholds and the constraints to RNA virus evolution Trends Microbiol 11 543–546 Occurrence Handle14659685 Occurrence Handle10.1016/j.tim.2003.10.006 Occurrence Handle1:CAS:528:DC%2BD3sXpsVSksb0%3D

    Article  PubMed  CAS  Google Scholar 

  • WW Hu SM Wong (1998) ArticleTitleThe use of DIG-labelled cRNA probes for the detection of Cymbidium mosaic potexvirus (CymMV) and Odotonglossum ringspot tobamovirus (ORSV) in orchids J Virol Methods 70 193–199 Occurrence Handle9562413 Occurrence Handle10.1016/S0166-0934(97)00187-0 Occurrence Handle1:CAS:528:DyaK1cXitVKhur8%3D

    Article  PubMed  CAS  Google Scholar 

  • RR Hudson DD Boos NL Kaplan (1992) ArticleTitleA statistical test for detecting geographic subdivision Mol Biol Evol 9 138–151 Occurrence Handle1552836 Occurrence Handle1:STN:280:By2B3czpvVA%3D

    PubMed  CAS  Google Scholar 

  • RR Hudson (2000) ArticleTitleA new statistic for detecting genetic differentiation Genetics 155 2011–2014 Occurrence Handle10924493 Occurrence Handle1:STN:280:DC%2BD3cvot1Kiuw%3D%3D

    PubMed  CAS  Google Scholar 

  • ML Izaguirre-Mayoral RC de Uzcategui O Carballo (1993) ArticleTitleCrassulacean acid metabolism in two species of orchids infected by Tobacco mosaic virus-orchid strain and or Cymbidium mosaic virus J Phytopathol 137 272–282 Occurrence Handle1:CAS:528:DyaK3sXkvFWnt7g%3D

    CAS  Google Scholar 

  • GM Jenkins EC Holmes (2003) ArticleTitleThe extent of codon usage bias in human RNA viruses and its evolutionary origin Virus Res 92 1–7 Occurrence Handle12606071 Occurrence Handle10.1016/S0168-1702(02)00309-X Occurrence Handle1:CAS:528:DC%2BD3sXhsVClsb4%3D

    Article  PubMed  CAS  Google Scholar 

  • DD Jensen (1950) ArticleTitleMosaic of Cymbidium orchids (Pacific Division Report) Phytopathology 40 966–967

    Google Scholar 

  • DD Jensen AH Gold (1955) ArticleTitleHosts, transmission, and electron microscopy of cymbidium mosaic virus with special reference to Cattleya leaf necrosis Phytopathology 45 327–334

    Google Scholar 

  • Kuhner M, Yamato J, Beerli P, Smith LP, Rynes E, Walkup E, Li C, Sloan J, Colacurcio P, Felsenstein J (2005) LAMARC v 2.0. University of Washington

  • F Leclercq Le Quillec C Riviere A Lagorce (2001) ArticleTitleSpread of Cymbidium mosaic potexvirus and potyviruses in vanilla plants grown in shade houses in Reunion Island Fruits (Paris) 56 249–260

    Google Scholar 

  • D Martin E Rybicki (2000) ArticleTitleRDP: detection of recombination amongst aligned sequences Bioinformatics 16 562–563 Occurrence Handle10980155 Occurrence Handle10.1093/bioinformatics/16.6.562 Occurrence Handle1:CAS:528:DC%2BD3cXnsVelsbc%3D

    Article  PubMed  CAS  Google Scholar 

  • M Nei S Kumar (2000) Molecular evolution and phylogenetics Oxford University Press New York

    Google Scholar 

  • MN Pearson JS Cole (1991) ArticleTitleFurther observations on the effects of cymbidium mosaic virus and odotonglossum ring spot virus on growth of Cymbidium orchids J Phytopathol 131 193–198

    Google Scholar 

  • X Perrier A Flori F Bonnot (2003) Data analysis methods P Hamon M Seguin X Perrier JC Glaszmann (Eds) Genetic diversity of cultivated tropical plants Enfield Science Publ., Montpellier France 43–76

    Google Scholar 

  • SE Ramos-Onsins J Rozas (2002) ArticleTitleStatistical properties of new neutrality tests against population growth Mol Biol Evol 19 2092–2100 Occurrence Handle12446801 Occurrence Handle1:CAS:528:DC%2BD38Xps12hsrc%3D

    PubMed  CAS  Google Scholar 

  • MJ Roossinck L Zhang K Hellwald (1999) ArticleTitleRearrangements in the 5′ nontranslated and phylogenetic analysis of Cucumber mosaic virus RNA3 indicate radial evolution of three subgroups J Virol 73 6752–6758 Occurrence Handle10400773 Occurrence Handle1:CAS:528:DyaK1MXksFKnurs%3D

    PubMed  CAS  Google Scholar 

  • J Rozas JC Sanchez-DelBarrio X Messeguer R Rozas (2003) ArticleTitleDnaSP, DNA polymorphism analyses by the coalescent and other methods Bioinformatics 19 2496–2497 Occurrence Handle14668244 Occurrence Handle10.1093/bioinformatics/btg359 Occurrence Handle1:CAS:528:DC%2BD3sXpvVSisLo%3D

    Article  PubMed  CAS  Google Scholar 

  • ML Seoh SM Wong L Zhang (1998) ArticleTitleSimultaneous TD/RT-PCR detection of cymbidium mosaic potexvirus and odontoglossum ringspot tobamovirus with a single pair of primer J Virol Methods 72 197–204 Occurrence Handle9694327 Occurrence Handle10.1016/S0166-0934(98)00018-4 Occurrence Handle1:CAS:528:DyaK1cXkvFWnsLk%3D

    Article  PubMed  CAS  Google Scholar 

  • P Simmonds DB Smith (1999) ArticleTitleStructural constraints on RNA virus evolution J Virol 73 5787–5794 Occurrence Handle10364330 Occurrence Handle1:CAS:528:DyaK1MXjvFyktro%3D

    PubMed  CAS  Google Scholar 

  • F Tajima (1989) ArticleTitleStatistical method for testing the neutral mutation hypothesis by DNA polymorphism Genetics 123 585–595 Occurrence Handle2513255 Occurrence Handle1:CAS:528:DyaK3cXhslentA%3D%3D

    PubMed  CAS  Google Scholar 

  • S Tanaka H Nishii S Ito M KameyaIwaki P Sommartya (1997) ArticleTitleDetection of Cymbidium mosaic potexvirus and Odontoglossum ringspot tobamovirus from Thai orchids by rapid immunofilter paper assay Plant Dis 81 167–170

    Google Scholar 

  • M Tsompana J Abad M Purugganan JW Moyer (2005) ArticleTitleThe molecular population genetics of the Tomato spotted wilt virus (TSWV) genome Mol Ecol 14 53–66 Occurrence Handle15643950 Occurrence Handle10.1111/j.1365-294X.2004.02392.x Occurrence Handle1:CAS:528:DC%2BD2MXhs1ejtbY%3D

    Article  PubMed  CAS  Google Scholar 

  • Van de Peer Y, De Wachter R (1993) TREECON: a software package for the construction and drawing of evolutionary trees. Comput Appl Biosci: 177–182

  • RAA Van der Vlugt M Berendsen (2002) ArticleTitleDevelopment of a general potexvirus detection method Eur J Plant Pathol 108 367–371 Occurrence Handle10.1023/A:1015644409484 Occurrence Handle1:CAS:528:DC%2BD38XkvFersLk%3D

    Article  CAS  Google Scholar 

  • J Verchot-Lubicz (2005) ArticleTitleA new cell to cell transport model for potexviruses Mol Plant Microbe Interact 18 283–290 Occurrence Handle15828680 Occurrence Handle1:CAS:528:DC%2BD2MXis1Ghs78%3D

    PubMed  CAS  Google Scholar 

  • GA Watterson (1975) ArticleTitleOn the number of segregating sites in genetical models without recombination Theor Popul Biol 7 256–276 Occurrence Handle1145509 Occurrence Handle10.1016/0040-5809(75)90020-9 Occurrence Handle1:STN:280:CSqC1MbgvF0%3D

    Article  PubMed  CAS  Google Scholar 

  • SM Wong PH Mahtani KC Lee HH Yu Y Tan KK Neo Y Chan M Wu CG Chng (1997) ArticleTitleCymbidium mosaic potexvirus RNA: complete nucleotide sequence and phylogenetic analysis – brief report Arch Virol 142 383–391 Occurrence Handle9125051 Occurrence Handle10.1007/s007050050084 Occurrence Handle1:CAS:528:DyaK2sXisVWrtrk%3D

    Article  PubMed  CAS  Google Scholar 

  • FW Zettler NJ Ko GC Wisler MS Elliott SM Wong (1990) ArticleTitleViruses of orchids and their control Plant Dis 74 621–626

    Google Scholar 

  • X Zeyong CM Higgins C Kunrong RG Dietzgen Z Zhongyi Y Liying F Xiao-Ping (1998) ArticleTitleEvidence for a third taxonomic subgroup of Peanut stunt virus from China Plant Dis 82 992–998

    Google Scholar 

  • H Zhou H Wang LF Huang M Naylor P Clifford (2005) ArticleTitleHeterogeneity in codon usages of sobemovirus genes Arch Virol 150 1591–1605 Occurrence Handle15834656 Occurrence Handle10.1007/s00705-005-0510-4 Occurrence Handle1:CAS:528:DC%2BD2MXmtlSqurY%3D

    Article  PubMed  CAS  Google Scholar 

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Authors and Affiliations

  1. CIRAD, UMR CIRAD-UR “Peuplements Végétaux et Bioagresseurs en Milieu Tropical”, Pôle de Protection des Plantes, Saint Pierre, La Réunion, France

    M. Moles & M. Grisoni

  2. Université de la Réunion, UMR CIRAD-UR “Peuplements Végétaux et Bioagresseurs en Milieu Tropical”, Saint Denis, La Réunion, France

    H. Delatte & K. Farreyrol

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  1. M. Moles
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Moles, M., Delatte, H., Farreyrol, K. et al. Evidence that Cymbidium mosaic virus (CymMV) isolates divide into two subgroups based on nucleotide diversity of coat protein and replicase genes. Arch Virol 152, 705–715 (2007). https://doi.org/10.1007/s00705-006-0897-6

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