Phylogenetic analysis of Potato virus Y (PVY) Isolates obtained in Potato (Solanum tuberosum) and Tamarillo (Solanum betaceum) crops from Colombia
DOI:
https://doi.org/10.17533/udea.acbi.329120Keywords:
capsid, Colombia, phylogeny, Potyvirus, SolanaceaeAbstract
Potato virus Y (PVY) is the most limiting virus in solanaceous crops worldwide. This virus is highly variable dueto a combination of high mutation and recombination rates. In this study, a phylogenetic analysis was performed on 24 PVY isolates obtained from potato and tamarillo crops from three regions of Colombia, using partial sequences of the viral coat (CP). Additionally, a complete gene sequence was obtained for 12 isolates and their similarities at the amino acid level were compared to PVY reference strains from the rest of the world. Our results revealed the presence of three main PVY variants in Colombia (named as I-Col, II-Int, and IV-Col). Two of them (I-Col y IV-Col) are not related to traditional PVY strains while II-Int is related to the PVYN/NTN clade. All three groups comprise sequences from potato and tamarillo, suggesting that both plants can act as alternative hosts to the same PVY genotypes. Amino acid analysis of CP confirmed the presence of three PVY variants; however variant I-Col showed affinity, although with low bootstrap values, to recombinant strains PVYNTN x PVYNE-11 from Brazil. The results indicate the need to adjust the systems for PVY detection and to undertake further biological studies of this virus in Colombia.
Downloads
References
Adams MJ, Antoniw JF, Fauquet CM. 2005. Molecular criteria for genus and species discrimination within the family Potyviridae. Archives of Virology, 150 (3): 459-479.
Álvarez J, Cotes JM., Marín M. 2011. Detección molecular de virus en material de siembra de tomate de árbol en Colombia. Revista de Protección Vegetal, 26 (2): 80-91.
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. 1990 Basic local alignment search tool. Journal of Molecular Biology, 215 (3): 403-410.
Ayala M, González P, Gutiérrez P, Cotes JM, Marín, M. 2010. Caracterización serológica y molecular de potyvirus asociados a la virosis del tomate de árbol en Antioquia (Colombia). Acta Biológica Colombiana, 15 (3): 143-162.
Balme-Sinibaldi V, Tribodet M, Croizat F, Lefeuvre P, Kerlan C, Jacquot E. 2006. Improvement of Potato virus Y (PVY) detection and quantitation using PVYN and PVYO specific real-time RT-PCR assays. Journal of Virological Methods, 134 (1): 261-266.
Blanco-Urgoiti B, Sanchez F, Dopazo J, Ponz F. 1996. A strain-type clustering of Potato virus Y based on the genetic distance between isolates calculated by RFLP analysis of the amplified CP gene. Archives of Virology, 141 (12): 2425-2442.
Blanco-Urgoiti B, Sánchez F, Pérez de San Roman C, Dopazo J, Ponz F. 1998. Potato virus Y group C isolates are a homogenous pathotype but two different genetic strains. Journal of General Virology, 79 (8): 2037-2042.
Boonham N, Barker I. 1998. Strain specific recombinant antibodies to Potato virus Y potyvirus. Journal of Virological Methods, 74 (4): 193-199.
Carrington JC, Haldeman R, Dolja VV, Restrepo-Hartwig MA. 1993. Internal cleavage and trans-proteolytic activities of the VPg-proteinase (NIa) of tobacco etch potyvirus in vivo. Journal of Virology, 67 (12): 6995-7000.
Cerovska, N. 1998. Production of monoclonal antibodies to potato virus Y NTN strain and their use for strain differentiation. Plant Pathology 47 (4): 505-509.
El-Absawy EA, Mahmoud A, Hemeida AA, Helmy M. 2012. Molecular Variation of Potato virus Y Isolated from Egypt. International Journal of Virology, 8 (1): 81-89.
Feki S, Bouslama L. 2008. Molecular phylogeny and genetic variability of the Potato virus Y (PVY) strains on the CP- encoding region. Annals of Microbiology, 58 (3): 433-437.
Felsenstein J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution, 39 (4): 783-791.
Galvino-Costa SBF, dos Reis Figueira A, Camargos VV, Geraldino PS, Hu XJ, Nikolaeva OV, Kerlan C, Karasev AV. 2012. A novel type of Potato virus Y recombinant genome, determined for the genetic strain PVYE. Plant Pathology, 61 (2): 388-398.
Gallo YM, Gutiérrez P, Marín M. 2012. Generación de anticuerpos policlonales para la detección de la variante genotípica GIII de PVY, en cultivos de tomate de árbol y papa de Colombia. Revista Colombiana de Biotecnología, 14 (1): 245-255.
Gil JF, Cotes JM, Marín M. 2011. Incidencia de potyvirus y caracterización molecular de PVY en regiones productoras de papa (Solanum tuberosum L.) de Colombia. Revista Colombiana de Biotecnología, 13 (1): 85-93.
Glais L, Tribodet M, Kerlan C. 2002. Genomic variability in Potato potyvirus Y (PVY): evidence that PVYNW and PVYNTN variants are single to multiple recombinants between PVYO and PVYN isolates. Archives of Virology, 147 (2): 363-378.
Glais L, Tribodet M, Kerlan C. 2005. Specific detection of the PVYNW variant of Potato virus Y. Journal of Virological Methods, 125 (2): 131-136.
Hall TA. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symposium Series, 41: 95-98.
Jacquot E, Tribodet M, Croizat F, Balme-Sinibaldi V, Kerlan C. 2005. A single nucleotide polymorphism-based technique for specific characterization of PVYO and PVYN isolates of Potato virus Y (PVY). Journal of Virological Methods, 125: 83-93.
Jaramillo MM, Gutiérrez P, Lagos LE, Cotes JM, Marín M. 2011. Detection of a complex of viruses in tamarillo (Solanum betaceum) orchards in the Andean region of Colombia. Tropical Plant Pathology, 36 (3): 150-159.
Kimura M. 1980. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16 (2): 111-120.
Lorenzen JH, Piche LM, Gudmestad NC, Meacham T, Shiel P. 2006. A multiplex PCR assay to characterize Potato virus Y isolates and identify strain mixtures. Plant Disease, 90 (7): 935-940.
Lorenzen J, Nolte P, Martin D, Pasche J, Gudmestad N. 2008. NE-11 represents a new strain variant class of Potato virus Y. Archives of Virology, 153 (3): 517-525.
Matthews REF. 1993. Diagnosis of plant virus diseases. Boca Ratón (EE. UU.): CRC Press. p. 374.
Moury B. 2010. A new lineage sheds light on the evolutionary history of Potato virus Y. Molecular Plant Pathology, 11 (1): 161-168.
Nie X, Singh RP. 2001. A novel usage of random primers for multiplex RT-PCR detection of virus and viroid in aphids, leaves, and tubers. Journal of Virological Methods, 91 (1): 37-49.
Nie X, Singh RP. 2003. Evolution on North American PVYNTN strains Tu 660 from local PVYN by mutation rather than recombination. Virus Genes, 26 (1): 39-47.
Saitou N, Nei M. 1987. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Molecular Biology and Evolution, 4 (4): 406-425. Schubert J, Fomitcheva V, Sztangret-Wisniewska J. 2007.
Diferentiation of Potato virus Y strains using improved sets of diagnostic PCR primers. Journal of Virological Methods, 140 (1): 66-74.
Shukla DD, Ward CW, Brunt AA. 1994. The Potyviridae. Wallingford (UK): CAB International. p. 516.
Sigvald R. 1984. The relative efficiency of some aphid species as vectors of Potato virus Y. Potato Research, 27 (3): 285-290.
Singh RP, McLaren DL, Nie X, Singh M. 2003. Possible escape of a recombinant isolate of Potato virus Y by serological indexing and methods of its detection. Plant Disease, 87 (6): 79-685.
Singh RP, Valkonen JPT, Gray SM, Boonham N, Jones RAC, Kerlan C, Schubert J. 2008. Brief review: The naming of Potato virus Y strains infecting potato. Archives of Virology, 153 (1): 1-13.
Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods.
Molecular Biology and Evolution, 28 (10): 2731-2739. Valkonen JPT. 2007. Potato viruses: Economical losses and biotechnological potential. En: Viola R, Gebhardt C, Govers F, Vreugdenhil D, MacKerron D, editores. Potato biology and biotechnology. San Diego (EE. UU.): Elsevier, p. 619-641.
Verchot J, Herndon KL, Carrington JC. 1992. Mutational analysis of the tobacco etch potyviral 35-kDa proteinase: identification of essential residues and requirements for autoproteolysis. Virology, 190 (1): 298-306.
Downloads
Published
How to Cite
Issue
Section
License
The authors exclusively authorize the Actualidades Biológicas journal to edit and publish the submitted manuscript if its publication is recommended and accepted, without this representing any cost to the Journal or the University of Antioquia.
All the ideas and opinions contained in the articles are sole responsibility of the authors. The total content of the issues or supplements of the journal is protected under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License, so they cannot be used for commercial purposes, but for educational purposes. However, please mention the Actualidades Biológicas journal as a source and send a copy of the publication in which the content was reproduced.
