Genome characterization of a Potato virus S (PVS) variant from tuber sprouts of Solanum phureja Juz. et Buk

Daniela Vallejo C.; Pablo Andrés Gutiérrez S.; Mauricio Marín M.

doi:10.15446/agron.colomb.v34n1.53161

Published

2016-01-01

Genome characterization of a Potato virus S (PVS) variant from tuber sprouts of Solanum phureja Juz. et Buk

Caracterización del genoma de una variante de Potato virus S (PVS) obtenida en brotes de tubérculos de Solanum phureja Juz. et Buk

DOI:

https://doi.org/10.15446/agron.colomb.v34n1.53161

Keywords:

plant viruses, carlaviruses, diagnostic techniques, ELISA, PCR, potatoes. (en)
virus de plantas, carlavirus, técnicas de diagnóstico, ELISA, PCR, papas (es)

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Authors

Daniela Vallejo C. Universidad Nacional de Colombia - Sede Medellín - Faculty of Sciences - Laboratory of Industrial Microbiology
Pablo Andrés Gutiérrez S. Universidad Nacional de Colombia - Sede Medellín - Faculty of Sciences - Laboratory of Industrial Microbiology
Mauricio Marín M. Universidad Nacional de Colombia - Sede Medellín - Faculty of Sciences - Laboratory of Cellular and Molecular Biology

Abstract (en)
Abstract (es)

Potato virus S (PVS) is a prevalent virus in potato fields in Colombia and the rest of the world. PVS has been classified into two separate lineages, PVSO (Ordinary) and PVSA (An- dean), which are genetically distinct. In this study, the com- plete genome sequence of a new PVS isolate (PVS_Antioquia) was obtained using High-throughput sequencing (Illumina HiSeq-2000) from tuber sprouts of Solanum phureja (var. Criolla Colombia). The PVS_Antioquia genome comprises 8,483 nt that code for six ORFs: RdRp (223 kDa), TGBp1-3 (25kDa, 12kDa, 7kDa) CP (32.3 kDa) and NABP (11 kDa) and share a high sequence identity with respect to the PVS_RVC (>95%) from Colombia, in contrast to 81 to 82% identity with respect to the PVSA and PVSO isolates from around the world. This genome information was used to design RT-qPCR primers that are specific for the Colombian PVS strains (RVC and Antioquia) which were validated in S. phureja leaf and tuber samples. These primers detected PVS in 80 and 60% of a set of fifteen leaf and tuber samples, respectively, suggesting a high incidence of this virus in the potato crops of Antioquia.

El Potato virus S (PVS) es un virus prevalente en los cultivos de papa de Colombia y otros lugares del mundo. Ha sido dividido en dos razas principales denominadas PVSO (Ordinaria) y PVSA (Andina), que representan a su vez dos linajes genéticos divergentes. En este trabajo se obtuvo la secuencia del genoma completo de un aislamiento de PVS denominado PVS_Antio- quia, por secuenciación masiva de nueva generación (Illumina HiSeq-2000) realizada sobre extractos de transcriptoma de tubérculos de Solanum phureja (var. Criolla Colombia). A partir de este genoma se diseñaron primers específicos para la detección por RT-qPCR de variantes colombianas de PVS (RVC y Antioquia), validándose su utilidad en pruebas de detección en tejido foliar y de tubérculos de S. phureja. El genoma de PVS_Antioquia tiene un tamaño de 8.483 nt que codifica para seis ORFs: RdRp (223 kDa), TGBp1-3 (25kDa, 12kDa, 7kDa) CP (32,3 kDa) y NABP (11 kDa), y comparte altos niveles de identidad con el aislamiento PVS_RVC (>95%) de Colombia y tan solo de 81 a 82% con representantes de PVSA y PVSO de diferentes países del mundo. Los primeros diseñados permitieron detectar el virus en 80 y 60% de 15 muestras foliares y 15 de tubérculos, respectivamente, lo que puede indicar la ocurrencia de altos niveles de incidencia de PVS y sus variantes en los cultivos de papa de Antioquia.

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