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Abstract Background Endogenous pararetroviral sequences (EPRVs) are a recently discovered class of repetitive sequences that is broadly distributed in the plant kingdom. The potential contribution of EPRVs to plant pathogenicity or, conversely, to virus resistance is just beginning to be explored. Some members of the family Solanaceae are particularly rich in EPRVs. In previous work, EPRVs have been characterized molecularly in various species of Nicotiana including N.tabacum (tobacco) and Solanum tuberosum (potato). Here we describe a family of EPRVs in cultivated tomato (Solanum lycopersicum L.) and a wild relative (S.habrochaites). Results Molecular cloning and DNA sequence analysis revealed that tomato EPRVs (named LycEPRVs) are most closely related to those in tobacco. The sequence similarity of LycEPRVs in S.lycopersicum and S.habrochaites indicates they are potentially derived from the same pararetrovirus. DNA blot analysis revealed a similar genomic organization in the two species, but also some independent excision or insertion events after species separation, or flanking sequence divergence. LycEPRVs share with the tobacco elements a disrupted genomic structure and frequent association with retrotransposons. Fluorescence in situ hybridization revealed that copies of LycEPRV are dispersed on all chromosomes in predominantly heterochromatic regions. Methylation of LycEPRVs was detected in CHG and asymmetric CHH nucleotide groups. Although normally quiescent EPRVs can be reactivated and produce symptoms of infection in some Nicotiana interspecific hybrids, a similar pathogenicity of LycEPRVs could not be demonstrated in Solanum L. section Lycopersicon [Mill.] hybrids. Even in healthy plants, however, transcripts derived from multiple LycEPRV loci and short RNAs complementary to LycEPRVs were detected and were elevated upon infection with heterologous viruses encoding suppressors of PTGS. Conclusion The analysis of LycEPRVs provides further evidence for the extensive invasion of pararetroviral sequences into the genomes of solanaceous plants. The detection of asymmetric CHH methylation and short RNAs, which are hallmarks of RNAi in plants, suggests that LycEPRVs are controlled by an RNA-mediated silencing mechanism.

Ficus carica is one of the most ancient cultivated crops, and is grown mainly in the Mediterranean region. In Austria, due to milder winters and longer warm periods than normal, figs are becoming more productive and popular among private growers. For future propagation of some fig varieties, the phytosanitary status of eight fig accessions, representing four Austrian genotypes maintained in a varietal collection plot, was investigated using PCR assays for presence of eight fig-infecting viruses. The four fig trees were infected with fig mosaic virus (FMV), fig badnavirus 1 (FBV-1), fig leaf mottle-associated virus 1 (FLMaV-1), fig mild mottle-associated virus (FMMaV) and fig fleck-associated virus (FFkaV); whereas fig leaf mottle-associated virus 2 (FLMaV-2), fig latent virus 1 (FLV-1) and fig cryptic virus 1 (FCV-1) were not detected. The sequences of PCR amplicons obtained from different viruses and samples showed greatest nucleotide variability of 0.5% for FBV-1, 12% for FLMaV-1, 16.3% for FMV, 14% for FMMaV, and 15% for FFkaV, when compared to their homologues in GenBank. A phylogenetic tree for FMV constructed based on partial RNA1 sequences showed that the Austrian isolates were most closely related to previously described Spanish and Greek isolates. The different symptoms observed in the tested trees were mainly in similar to with those reported for FMV, the agent of fig mosaic disease. This is the first report on the presence of fig mosaic-associated viruses in Austria. [ABSTRACT FROM AUTHOR]