Abstract
BackgroundEndogenous 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).ResultsMolecular 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.ConclusionThe 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.
Highlights
Endogenous pararetroviral sequences (EPRVs) are a recently discovered class of repetitive sequences that is broadly distributed in the plant kingdom
LycEPRV identification, isolation and sequence analysis Tomato EPRVs were originally detected by DNA blot analysis using a 5.5 kb DNA fragment of NsEPRV (Nicotiana sylvestris EPRV), one of three EPRV families in tobacco [1,2], to probe DNA prepared from various species of Solanum
This pattern is reminiscent of that observed with Nicotiana species [1] and suggests a dispersed organization of multiple copies of a related EPRV family
Summary
Endogenous pararetroviral sequences (EPRVs) are a recently discovered class of repetitive sequences that is broadly distributed in the plant kingdom. Plant pararetroviruses (Caulimoviridae) have doublestranded DNA genomes and are considered retroelements because they use reverse transcription for replication Unlike other retroelements, such as retroviruses and retrotransposons, integration into the host genome is not essential during their replication cycle. In recent years there have been accumulating reports of endogenous pararetroviral sequences (EPRVs) in the nuclear genomes of several plants including tobacco (Nicotiana tabacum) and other Nicotiana species [1,2,3], potato [4], banana [5,6,7], petunia [8] and rice [9]. Current information suggests that EPRVs are not always neutral components of plant genomes but can potentially contribute to either pathogenicity or virus resistance in the host. Interspecific crosses and in vitro propagation can induce EPRV reactivation, which has been shown to be economically detrimental in banana breeding [2,6,11,12,13]
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