title: Genetic variability within the Polish tomato torrado virus Kra isolate caused by deletions in the 3'-untranslated region of genomic RNA1.
abstract: Tomato torrado virus (ToTV) is in the genus Torradovirus in the family Secoviridae. ToTV contains a single-stranded, positive-sense, bipartite RNA genome encapsidated in icosahedral particles. It is a serious tomato pathogen causing significant crop reductions. Its occurrence has been reported from many countries worldwide. However, the state of knowledge of ToTV epidemiology, sequences and phylogeny is still rather poor. In this study we found that the Polish ToTV isolates are characterized by significant genetic variability of the 3'-untranslated region (UTR) of RNA1. The high resolution melting real-time PCR approach showed the presence of genetic variants within Polish ToTV isolates purified from Nicotiana benthamiana. Further sequencing of Kra ToTV revealed five genetic variants of RNA1 within the isolate differing in the 3'-untranslated region length resulting from deletions ranging from 6 to 163 nucleotides. In light of the published studies, the genetic variability of ToTV associated with large deletions within an isolate may not necessarily be rare and may influence the virus evolution and adaptation.
authors.affiliation: Interdepartmental Laboratory of Molecular Biology, Institute of Plant Protection - National Research Institute, W. Wegorka 20, 60-318 Poznań, Poland.
authors.forename: Marta
authors.initials: M
authors.lastname: Budziszewska
authors.affiliation: Interdepartmental Laboratory of Molecular Biology, Institute of Plant Protection - National Research Institute, W. Wegorka 20, 60-318 Poznań, Poland.
authors.forename: Przemysław
authors.initials: P
authors.lastname: Wieczorek
authors.affiliation: Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, TU Muenchen Maximus-von-Imhof-Forum 3, 85354 Freising, Germany.
authors.forename: Yanping
authors.initials: Y
authors.lastname: Zhang
authors.affiliation: Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, TU Muenchen Maximus-von-Imhof-Forum 3, 85354 Freising, Germany; Helmholtz Center Munich - German Research Center for Environmental Health (GmbH), Institute of Bioinformatics and Systems Biology, Ingolstaaedter Landstraße 1, D-85764 Neuherberg, Germany.
authors.forename: Dmitrij
authors.initials: D
authors.lastname: Frishman
authors.affiliation: Interdepartmental Laboratory of Molecular Biology, Institute of Plant Protection - National Research Institute, W. Wegorka 20, 60-318 Poznań, Poland. Electronic address: ao.steplowska@iorpib.poznan.pl.
authors.forename: Aleksandra
authors.initials: A
authors.lastname: Obrępalska-Stęplowska
mesh_terms: D020413:3' Untranslated Regions; D001483:Base Sequence; D014644:Genetic Variation; D018551:Solanum lycopersicum / Q000821:virology*; D008969:Molecular Sequence Data; D010849:Picornaviridae / Q000235:genetics*; D010935:Plant Diseases / Q000821:virology*; D012367:RNA, Viral / Q000235:genetics*; D017384:Sequence Deletion
chemical_list: D020413:3' Untranslated Regions; D012367:RNA, Viral
keywords: 3′Untranslated region; Genomic diversity; Large deletions; Repeated sequences; Tomato torrado virus