Screening of some Croatian autochthonous grapevine varieties reveals a multitude of viruses, including novel ones
Next-generation sequencing of total RNA samples from four Croatian autochthonous grapevine varieties revealed the presence of a novel virus in two grapevine accessions. The complete genome sequence of a novel virus, tentatively named “grapevine badnavirus 1” (GBV-1), was reconstructed from a de novo-assembled contig. GBV-1 has a genome of 7,145 nucleotides containing three ORFs with sequence similarity to other badnaviruses. In addition, several other viruses and viroids, including grapevine virus G, grapevine virus K/D, grapevine virus T, grapevine Roditis leaf discoloration-associated virus, grapevine yellow speckle viroids 1 and 2, and hop stunt viroid were detected and identified for the first time in Croatian grapevines in the course of this study.
The research leading to these results received funding from the European Union Seventh Framework Programme (FP7 2007-2013) under Grant agreement no. 291823 Marie Curie FP7-PEOPLE-2011-COFUND (The New International Fellowship Mobility Programme for Experienced Researchers in Croatia - NEWFELPRO). This article was prepared as a part of a project “Ecology of an emerging grapevine virus in Croatia and California (EcoGVCC)” which received funding through NEWFELPRO under Grant agreement no. 51. The work used the Vincent J. Coates Genomics Sequencing Laboratory at UC Berkeley, supported by NIH S10 OD018174 Instrumentation Grant. Special thanks to Dijana Škorić and Cecilia Prator for critical review of the manuscript, and Mladen Poletti Kopešić for technical support.
Compliance with ethical standards
Conflict of interest
The authors (DV and RA) declare that they have no conflict of interest.
This article does not contain any studies with human participants or animals performed by any of the authors.
- 3.Vončina D, Đermić E, Cvjetković B, Maletić E, Pejić I, Karoglan Kontić J (2009) Occurrence of the important grapevine viruses in population of Croatian autochthonous grapevine varieties from Kaštela region. In: 32nd World Congress of vine and wine, 7th general assembly of the OIV and Wine Kubanović, Veronika (ed.). Zagreb: Ministarstvo poljoprivrede, ribarstva i ruralnog razvoja:199–200Google Scholar
- 4.Joshi NA, Fass JN (2011) Sickle: a sliding-window, adaptive, quality-based trimming tool for FastQ files (Version 1.33) [Software]. https://github.com/najoshi/sickle
- 8.Nurk S, Bankevich A, Antipov D, Gurevich A, Korobeynikov A, Lapidus A, Prjibelsky A, Pyshkin A, Sirotkin A, Sirotkin Y, Stepanauskas R, McLean J, Lasken R, Clingenpeel SR, Woyke T, Tesler G, Alekseyev MA, Pevzner PA (2013) Assembling genomes and mini-metagenomes from highly chimeric reads. Res Comp Mol Biol 7821:158–170Google Scholar
- 12.Geering ADW, Hull R (2012) Family Caulimoviridae. In: King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ (eds) Virus taxonomy. 9th report of the international committee on taxonomy of viruses. Elsevier Academic Press, London, pp 429–443Google Scholar
- 18.Šarić A, Krajačić M, Škorić D (1996) Viroidi kao patogeni poljoprivrednih kultura u Hrvatskoj. 40. seminar iz zaštite bilja. Opatija, Glasnik Zaštite Bilja 1:6–7Google Scholar