Detection of RNA viruses in tomato crops from eastern Antioquia (Colombia) using next-generation sequencing (NGS)

Authors

  • Yuliana Gallo García Facultad de Medicina, Universidad CES, Medellín, Colombia.
  • Laura Muñoz Baena Laboratorio de Microbiología Industrial, Facultad de Ciencias, Universidad Nacional de Colombia Sede Medellín, Colombia.
  • Luisa F. Toro Fernández Laboratorio de Microbiología Industrial, Facultad de Ciencias, Universidad Nacional de Colombia Sede Medellín, Colombia.
  • Pablo A. Gutiérrez Sánchez Laboratorio de Microbiología Industrial, Facultad de Ciencias, Universidad Nacional de Colombia Sede Medellín, Colombia.
  • Mauricio Marín Montoya Laboratorio de Biología Celular y Molecular, Facultad de Ciencias, Universidad Nacional de Colombia Sede Medellín, Colombia.

Keywords:

Carlavirus, Potexvirus, RT-PCR, sequencing, Solanum lycopersicum

Abstract

Viral diseases are one of the most important limiting factors of the production of tomato. In the world about 136 viral species have been reported to infect this plant but only 15 have been registered in Colombia, thus far. The latter suggests that the tomato virome in Colombia is underrepresented. In this work, the diversity of RNA viruses infecting tomato var. Chonto crops in eastern Antioquia was evaluated by RT-PCR, RT-qPCR, Next-generation sequencing (NGS) and Sanger sequencing. NGS revealed the presence  of  Potato  virus  Y (PVY), Potato  yellow  vein  virus (PYVV), Potato  virus  S (PVS)  and  Potato virus X (PVX). PVX (6428 nt) and PVS (8492 nt) were the most abundant viruses and were completely assembled using the RNA-seq data. Infection by all four viruses was confirmed by RT-qPCR and Sanger sequencing of RT-PCR amplicons. These results highlight the need to strengthen the integrated disease management program for tomato in Colombia. This work is the first formal report of PVS and PVX naturally infecting tomato in Colombia.

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Published

2020-10-01

Issue

Vol. 32 No. 3 (2020): Septiembre-Diciembre

Section

Artículos

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How to Cite

Detection of RNA viruses in tomato crops from eastern Antioquia (Colombia) using next-generation sequencing (NGS). (2020). Bioagro, 32(3), 147-158. https://revistas2.uclave.org/index.php/bioagro/article/view/2757