Raspberry bushy dwarf virus in Slovenia - geographic distribution, genetic diversity and population structure
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Raspberry bushy dwarf virus in Slovenia - geographic distribution, genetic diversity and population structure Irena Mavrič Pleško & Janja Lamovšek & Andreja Lešnik & Mojca Viršček Marn
Received: 21 April 2020 / Revised: 16 July 2020 / Accepted: 10 September 2020 # The Author(s) 2020
Abstract Raspberry bushy dwarf virus (RBDV) is a long-known virus naturally infecting Rubus and grapevine. It is also one of the economically most important viruses of raspberries, but there are only a limited number of sequences covering a substantial part of the genome available in the databases. The aim of this study was: i) to study the geographic distribution of RBDV in Slovenia, and ii) to sequence RNA2 of several red raspberry and grapevine RBDV isolates and study their phylogeny and population structure. Geographic distribution studies were performed over a period of 13 years in three wine-growing regions of Slovenia (Primorska, Podravje and Posavje). The highest incidence of RBDV was found in Podravje (58.8%) and the lowest in Primorska (5.1%). Big differences were observed between Vipavska dolina (10.2%) and three other winegrowing districts of Primorska region (0.4–1.2%). Almost complete RNA2 sequences were obtained for four red raspberry isolates and seven grapevine isolates. Additionally, only coat protein sequences were obtained for three red raspberry isolates. Phylogenetic and population diversity analyses were performed on all available RBDV sequences. Phylogenetic analysis has shown clear differences in sequences from Rubus and grapevine that form two highly supported clades. In RNA2 I. Mavrič Pleško (*) : J. Lamovšek : M. Viršček Marn Agricultural Institute of Slovenia, Hacquetova 17, SI-1000 Ljubljana, Slovenia e-mail: [email protected] A. Lešnik SI-2211 Pesnica pri Mariboru, Maribor, Slovenia
analysis additional two sub-clades were found in grapevine clade. Two major subclades were identified also in the Rubus clade with further differentiation within these subclades. Purifying or stabilizing selection was found to be acting on both, CP and MP genes while few codons were found to be under positive selection. Keywords RBDV . Population structure . Grapevine . Rubus . Genetic diversity . Selection pressure
Raspberry bushy dwarf virus (RBDV) is a well-studied virus found naturally in raspberries, blackberries and grapevines (reviewed in Martin et al. 2013). In red raspberries, RBDV has long been implicated in crumbly fruit disease, which has been shown to be more severe in mixed infections with one or more aphid transmitted viruses (Martin et al. 2013; Quito-Avila et al. 2014). RBDV, a sole member of the genus Idaeovirus, is pollen transmitted. Natural infection with RBDV has long been confined to Rubus spp. while experimental host range is wider (Jones et al. 1982). The RBDV presence in Rubus spp. has been reported from Europe, North America, South America, South Africa, Japan and New Zealand (Barbara et al. 2001; Dal Zotto et al. 2017; Dulić-Marković and Ranković 1992; Isogai et al. 2012; Kooyman et al. 1982; M
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