The complete nucleotide sequence and genome organization of Fig cryptic virus, a novel bipartite dsRNA virus infecting fig, widely distributed in the Mediterranean basin

Abstract

Two double-stranded RNA (dsRNA) segments of a virus with a bipartite genome identified in fig (Ficus carica L.) and denoted Fig cryptic virus (FCV) were cloned and sequenced. Viral dsRNAs are 1696 bp (RNA-1) and 1415 bp (RNA-2) in size. RNA-1 contains a single ORF (1419 nt) potentially encoding a 54 kDa protein and comprising the conserved amino acid motifs of the RNA-dependent RNA polymerase (RdRp) domain of species of the genus Alphacryptovirus. Its full-length amino acid sequence has the highest identity with Raphanus sativus cryptic virus 2 (RsCV-2) (36%), Beet cryptic virus 3 (BCV-3) (36%) and Fragaria chiloensis cryptic virus (FCCV) (34%). RNA-2 has also a single ORF (1014 nt) coding for a polypeptide with a predicted molecular mass of 38 kDa, identified as the viral coat protein (CP). In a phylogenetic tree constructed with the amino acid sequences of the RdRp domain, FCV clusters in a clade comprising BCV-3 and a number of tentative species of the genus Alphacryptovirus. FCV is not mechanically transmissible. It was detected in fig orchards of six Mediterranean countries (Albania, Algeria, Italy, Lebanon, Syria and Tunisia) where it does not seem to induce a visible disease.

Efficacy of Tissue Culture in Virus Elimination from Caprifig and Female Fig Varieties (Ficus carica L.)

“…Actually, ten viruses, of different genera, associated to FMD have been identified in fig trees: Emaravirus, FMV; Ampelovirus, Fig leaf mottle-associated virus-2 (FLMaV-2); Trichovirus, Fig latent virus-1 (FLV-1); Closterovirus, Fig leaf mottle-associated virus-1 (FLMaV-1), Arkansas fig closterovirus-1 (AFCV-1), Arkansas fig closterovirus-2 (AFCV-2), and Fig milde-mottle-associated virus (FMMaV); Alphacryptovirus, Fig cryptic virus (FCV); Maculavirus, Fig fleck associated virus (FFkaV); and Badnavirus, Fig badnavirus-1 (FBV-1) (Elbeaino et al, 2007, 2009a, 2011a, 2011b; Gattoni et al, 2009; Laney et al, 2012; Tzanetakis et al, 2010). …”

“…In Tunisia, viruses reported to be associated to FMD are: FLMaV-1 (Nahdi et al, 2006), FLMaV-2 (Elbeaino et al, 2009b), FCV and FFkaV (Elbeaino et al, 2011a, 2011b), FMV (Elair et al, 2012), and FMMaV and FLV-1 (Elair et al, 2013). The FCV and the FMMaV were mentioned to be spread in many Tunisian fig orchards with relatively high infection rates (17.5% and 10.7%, respectively) (Elair et al, 2015; Elbeaino et al, 2011a), which inhibits the development of healthy orchards and limits the production.…”

“…The FCV and the FMMaV were mentioned to be spread in many Tunisian fig orchards with relatively high infection rates (17.5% and 10.7%, respectively) (Elair et al, 2015; Elbeaino et al, 2011a), which inhibits the development of healthy orchards and limits the production. Meristem culture, as an effective tool for virus eradication from horticultural plants (Comlekcioglu et al, 2007; Miloŝević et al, 2012) is also applied for the production of virus-free fig plants and particularly FCV and FMMaV-free fig trees.…”

Use of standard and setup of non conventional techniques for the elimination of viruses associated with Fig Mosaic Disease (FMD) in fig germplasm (Ficus carica L.)

“…FCV is the first virus of the family Partitiviridae to be detected in fig trees and one of the few infecting woody crops in nature (Elbeaino et al, 2011c). Cryptic viruses are members of the family Partitiviridae, which comprises isometric viruses infecting monocotyledonous and dicotyledonous plant species, currently classified in the genera Alphacryptovirus and (Ghabrial et al, 2005).…”

“…This family also embraces the genera Partitivirus and Cryspovirus which include fungal and protozoan dsRNA viruses, respectively (Nibert et al, 2009). Plant-infecting members of the family Partitiviridae are transmitted through seeds and pollen but not by grafting or mechanical inoculation, and occur in very low concentration in the host plant (Ghabrial et al, 2005), and apparently have no economic impact (Elbeaino et al, 2011c).…”