Genome Sequencing of Potato yellow vein virus (PYVV) Strain Infecting Solanum lycopersicum in Colombia

Abstract

Potato yellow vein virus (PYVV) is one of the most important pathogens of potato in the Andean region. In spite of having been detected in tomato crops in Colombia, knowledge on the biological characteristics of PYVV is limited on this host. In this study, next-generation sequencing (NGS) of a PYVV strain infecting tomato in Marinilla District (Antioquia) was performed; additionally, three primer set useful in RT-PCR and RT-qPCR detection were also tested. The consensus genome consisted of three RNA segments of 8043 nt (RNA1), 5346 nt (RNA2) and 3896 nt (RNA3) encoding ten ORF with slight lower sequence identity in relation to PYVV isolates from potato. Sequence analysis suggests the presence of regions potentially undergoing positive selection in the ORFs coding for MET/HEL and CPm possibly as a result of host adaptation. Experimental validation of primers resulted in amplicon with the expected size while melting temperature analysis and sequencing suggest the presence of at least two PYVV infecting S. lycopersicum in east Antioquia in agreement with the NGS data.

Keywords

• Crinivirus
• RT-PCR
• RT-qPCR
• secuenciación de nucleótidos de alto rendimiento
• Solanaceae.