Partial molecular characterization of begomoviruses isolated from weeds collected in tomato crops in the southeast of Valle del Cauca, Colombia

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Juan Carlos Vaca-Vaca
Frenyiline Jara-Tejada
Karina López-López


Weeds are a source of new viruses but are often neglected during diversity studies. Eleven weed samples previously were collected along the edges of tomato crops in four municipalities (Florida, Ginebra, Cerrito and Candelaria) in the southeast of Valle del Cauca. These samples were positive for begomoviruses, but their molecular characterization had not been done until now. For each sample, DNA fragments were cloned, sequenced and analyzed. Nucleotide sequence analysis of viral fragments showed the presence of six different begomoviruses: two viruses isolated from Lantana camara, Desmodium sp. and Amaranthus dubius, which were previously identified as potato yellow mosaic virus (PYMV) and passionfruit leaf distortion virus (PLDV), respectively; four viruses isolated from L. camara, A. dubius, Rivina humilis, Desmodium sp., Rhynchosia minima, Hybanthus attenuatus, Verbena sp., Croton hirtus and Caesalpinia sp., showed the highest nucleotide sequence identity (89%) with the bean chlorotic mosaic virus (BChMV), datura leaf distortion virus (DaLDV) and rhynchosia golden mosaic Yucatan virus (RhGMYV). The cloned virus fragments isolated from these weeds could be new begomoviruses which have not been previously reported before, according with the ICTV species demarcation criteria established for the Begomovirus genera (≥91 % sequence identity). In this study, mixed infections of begomoviruses were founded in Desmodium sp. and A. dubius. Finally, this paper reports for the first time the identification of three alternative begomovirus weeds: A. dubius for PYMV and L. camara and Desmodium sp. for PLDV, both viruses which infect tomato and passion fruit crops, respectively.


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Alves-Júnior, M., A. Poliane-Zerbini, E. Andrade, D. Esposito, F. Silva, A.C.F. da Cruz, M.C. Ventrel, W. Otoni, and M. Zerbini. 2009. Synergism and negative interference during co-infection of tomato and Nicotiana benthamiana with two bipartite begomoviruses. Virology 387(2), 257-266. Doi: 10.1016/j.virol.2009.01.046

Andrade, E.C., G.G. Manhani, P.F. Alfenas, R.F. Calegario, E.P.B. Fontes, and F.M. Zerbini. 2006. Tomato yellow spot virus a tomato infecting begomovirus from Brazil with a closer relationship to viruses from Sida sp. forms pseudorecombinants with begomoviruses from but not from Sida. J. Gen. Virol. 87(12), 3687-3696. Doi: 10.1099/vir.0.82279-0

Barreto, S.S., M. Hallwass, O.M. Aquino, and K. Inoue-Nagata. 2013. A study of weeds as potential inoculum sources for a tomato-infecting begomovirus in central Brazil. Phytopathol. 103(5), 436-44. Doi: 10.1094/PHYTO-07-12-0174-R

Brown, J.K., F.M. Zerbini, J. Navas-Castillo, E. Moriones, R. Ramos-Sobrinho, J.C. Silva, E. Fiallo-Olivé, R.W. Briddon, C. Hernandez-Zepeda, A. Idris, V.G. Malathi, D.P. Martin, R. Rivera-Bustamante, S. Ueda, and A. Varsani. 2015. Revision of begomovirus taxonomy based on pairwise sequence comparisons. Arch. Virol. 160(6), 1593-1619. Doi: 10.1007/s00705-015-2398-y

Carvajal-Yepes, M., L. Zambrano, J.M. Bueno, B. Raatz, and W.J. Cuellar. 2017. Complete genome sequence of bean leaf crumple virus, a novel begomovirus infecting common bean in Colombia. Arch. Virol. 162(6), 1773-1776. Doi: 10.1007/s00705-015-2398-y

Da Silva, S.C., G.P. Castillo-Urquiza, B.T. Hora Júnior, I.P. Assunção, G.S.A. Lima, G. Pio-Ribeiro, E.S.G. Mizubuti, and F.M. Zerbini. 2011. High genetic variability and recombination in a begomovirus population infecting the ubiquitous weed Cleome affine in northeastern Brazil. Arch. Virol. 156(12), 2205-2213. Doi: 10.1007/s00705-011-1119-4

Fargette, D., G. Konate, C. Fauquet, E. Muller, M. Petersmith, and M. Thresh. 2006. Molecular ecology and emergence of tropical viruses. Annu. Rev. Phytopathol. 44, 235-260. Doi: 10.1146/annurev.phyto.44.120705.104644

Ferro, C., J. Silva, C. Xavier, M. Godinho, A. Lima, T. Mar, D. Lau, and F. Zerbini. 2017. The ever increasing diversity of begomoviruses infecting non-cultivated hosts: new species from Sida spp. and Leonurus sibiricus, plus two New World alphasatellites. Ann. Appl. Biol. 170(2), 204-218. Doi: 10.1111/aab.12329

Fiallo-Olivé, E., D.T. Chirinos, F. Geraud-Pouey, E. Moriones, and J. Navas-Castillo. 2013a. Complete genome sequences of two begomoviruses infecting weeds in Venezuela. Arch. Virol. 158(1), 277-280. Doi: 10.1007/s00705-012-1451-3

Fiallo-Olivé, E., B. Márquez-Martín, I. Hassan, D.T. Chirinos, F. Geraud-Pouey, E. Moriones, and J. Navas-Castillo. 2013b. Complete genome sequences of two novel begomoviruses infecting common bean in Venezuela. Arch. Virol. 158(3), 723-727. Doi: 10.1007/s00705-012-1545-y

Fondong, V.N. 2013. Geminivirus protein structure and function. Mol. Plant Pathol. 14(6), 635-649. Doi: 10.1111/mpp.12032

Gallo, Y., L.F. Toro, H. Jaramillo, P.A. Gutiérrez, and M. Marín. 2018. Identificación y caracterización molecular del genoma completo de tres virus en cultivos de lulo (Solanum quitoense) de Antioquia (Colombia). Rev. Colomb. Cienc. Hortic. 12(2), 281-292. Doi: 10.17584/rcch.2018v12i2.7692

García-Andrés, S., G.P. Accotto, J. Navas-Castillo, and E. Moriones. 2006. Begomovirus genetic diversity in the native plant reservoir Solanum nigrum: evidence for the presence of a new virus species of recombinant nature. Virology 350(2), 433-442. Doi: 10.1016/j.virol.2006.02.028

Gilbertson, R.L., O. Batuman, C.G. Webster, and S. Adkins. 2016. Role of the insect supervectors Bemisia tabaci and Frankliniella occidentalis in the emergence and global spread of plant viruses. Annu. Rev. Virol. 2(1), 67-93. Doi: 10.1146/annurev-virology-031413-085410

Gilbertson, R.L., J.C. Faria, S.F. Hanson, F.I. Morales, P. Ahlquist, D.P. Maxwell, and D.R. Russell. 1991. Cloning of the complete. DNA genomes of four bean-infecting geminiviruses and determining their infectivity by electric discharge particle acceleration. Phytopathology 81(9), 980- 985. Doi: 10.1094/Phyto-81-980

Hernández-Zepeda, C., J.K. Brown, O.A. Moreno-Valenzuela, G. Argüello-Astorga, A.M. Idris, G. Carnevali, and R.F. Rivera-Bustamante. 2010. Characterization of Rhynchosia yellow mosaic Yucatan virus, a new recombinant begomovirus associated with two fabaceous weeds in Yucatan, Mexico. Arch. Virol. 155(10), 1571-1579. Doi: 10.1007/s00705-010-0730-0

Jordá, C., I. Font, P. Martínez, M. Juarez, A. Ortega, and A. Lacasa. 2007. Current status and new natural hosts of Tomato yellow leaf curl virus (TYLCV) in Spain. Plant Dis. 85(4), 445. Doi: 10.1094/PDIS.2001.85.4.445C

Kumar, S., G. Stecher, and K. Tamura. 2016. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol. Biol. Evol. 33(7), 1870-1874. Doi: 10.1093/molbev/msw054

López-López, K., F. Jara-Tejada, and J.C. Vaca-Vaca. 2014. Nuevos hospederos alternativos de begomovirus identificados en valle del cauca. Rev. Fitopatol. Colomb. 38(1), 19-23.

López-López, K., F. Jara-Tejada, and J.C. Vaca-Vaca. 2019. Molecular characterization of a new begomovirus isolated from five weeds species collected in tomato crops in Valle del Cauca. Acta Biol. Colomb. 24(3), 528-537. Doi: 10.15446/abc.v24n3.79366

López-López, K., D. Otavo-Fiscal, and J.C. Vaca-Vaca. 2012. Búsqueda de hospederos alternativos del virus del mosaico amarillo de la papa, un begomovirus que afecta cultivos de tomate en el Valle del Cauca. Acta Agron. 61(5), 24-25.

Martínez, A.K., F.J. Morales, and F.A. Cabrera. 2008. Caracterización molecular de un begomovirus del tomate en el Valle del Cauca, Colombia, y búsqueda de fuentes de resistencia para el mejoramiento de la variedad Unapal Maravilla. Acta Agron. 57(3), 167-174.

Monde, G., J. Walangululu, S. Winter, and C. Bragard. 2010. Dual infection by cassava begomoviruses in two leguminous species (Fabaceae) in Yangambi, Northeastern Democratic Republic of Congo. Arch. Virol. 155(11), 1865-1869. Doi: 10.1007/s00705-010-0772-3

Muhire, B.M., A. Varsani, and D.P. Martin. 2014. SDT: A virus classification tool based on pairwise sequence alignment and identity calculation. Plos ONE 9, e108277. Doi: 10.1371/journal.pone.0108277

Padidam, M., S. Sawyer, and C.M. Fauquet. 1999. Possible emergence of new geminiviruses by frequent recombination. Virology 265(2), 218-225. Doi: 10.1006/viro.1999.0056

Prajapat, R., A. Marwal, and R.K. Gaur. 2014. Begomovirus associated with alternative host weeds: a critical appraisal. Arch. Phytopathol. Pflanzenschutz. 47(2), 157-170. Doi: 10.1080/03235408.2013.805497

Rentería-Canett, I., B. Xoconostle-Cázares, R. Ruiz-Medrano, and R.F. Rivera-Bustamante. 2011. Geminivirus mixed infection on pepper plants: synergistic interaction between PHYVV and PepGMV. Virol. J. 8(1), 104. Doi: 10.1186/1743-422X-8-104

Rojas, M., R. Gilbertson, and D. Maxwell. 1992. Use of degenerate primers in the polymerase chain reaction to detect whitefly-transmitted Geminiviruses. Plant Dis. 77, 340-347. Doi: 10.1094/PD-77-0340

Sanchez-Campos S., J. Navas-Castillo, F. Monci, J.A. Diaz, and E. Moriones. 2000. Mercurialis ambigua and Solanun luteum: two newly discovered natural host of Tomato yellow leaf curl geminivirus. Eur. J. Plant Pathol. 106(4), 391-394. Doi: 10.1023/A:1008758622582

Sanz, A.I., A. Fraile, F. García-Arenal, X. Zhou, D.J. Robinson, S. Khalid, T. Butt, and B.D. Harrison. 2000. Multiple infection, recombination and genome relationships among begomovirus isolates found in cotton and other plants in Pakistan. J. Gen. Virol. 81(7), 1839-1849. Doi: 10.1099/0022-1317-81-7-1839

Vaca-Vaca, J.C., J.F. Betancur-Pérez, and K. López-López. 2012. Distribución y diversidad genética de begomovirus que infectan tomate (Solanum lycopersicum L.) en Colombia. Rev. Colomb. Biotecnol. 14(1), 60-76.

Vaca-Vaca, J.C., E.C. Carrasco-Lozano, and K. López-López. 2017. Molecular identification of a new begomovirus infecting yellow passion fruit (Passiflora edulis) in Colombia. Arch. Virol. 162(2), 573-576. Doi: 10.1007/s00705-016-3098-y

Vaca-Vaca, J.C., V. Corredor-Saenz, F. Jara-Tejada, D. Betancourt-Andrade, and K. López-López. 2019a. Nuevos hospederos alternativos de begomovirus asociados al cultivo de ají en el Valle del Cauca. Acta Agron. 68(1), 56-60. Doi: 10.15446/acag.v68n1.77487

Vaca-Vaca, J.C., F. Jara-Tejada, and K. López-López. 2018. Croton golden mosaic virus: a new bipartite begomovirus isolated from Croton hirtus in Colombia. Arch. Virol. 163(11), 3199-3202. Doi: 10.1007/s00705-018-3989-1

Vaca-Vaca, J.C., J. Morales-Euse, D.M. Rivera-Toro, and K. López-López. 2019b. Primer reporte de begomovirus infectando cultivos de ají (Capsicum spp.) en Colombia. Acta Biol. Colomb. 24(3), 452-462. Doi: 10.15446/abc.v24n3.79367

Zerbini, F.M., R.W. Briddon, A. Idris, D.P. Martin, E. Moriones, J. Navas-Castillo, R. Rivera-Bustamante, P. Roumagnac, and A. Varsani. 2017. ICTV virus taxonomy profile: Geminiviridae. J. Gen. Virol. 98(2), 131-133. Doi: 10.1099/jgv.0.000738

Zhang, Z., S. Schwartz, L. Wagner, and W. Miller. 2000. A greedy algorithm for aligning DNA sequences. J. Comput. Biol. 7(1-2), 203-214. Doi: 10.1089/10665270050081478


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