title: Endogenous pararetroviral sequences in tomato (Solanum lycopersicum) and related species.
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.
  
  
  CONCLUSIONS
  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.
authors.affiliation: Gregor Mendel Institute of Plant Molecular Biology (GMI), Wien, Austria. christina.staginnus@gmi.oeaw.ac.at
authors.forename: Christina
authors.initials: C
authors.lastname: Staginnus
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Gregor
authors.forename: M Florian
authors.initials: MF
authors.lastname: Mette
authors.forename: Chee How
authors.initials: CH
authors.lastname: Teo
authors.forename: Eduviges Glenda
authors.initials: EG
authors.lastname: Borroto-Fernández
authors.forename: Margit Laimer da Câmara
authors.initials: ML
authors.lastname: Machado
authors.forename: Marjori
authors.initials: M
authors.lastname: Matzke
authors.forename: Trude
authors.initials: T
authors.lastname: Schwarzacher
mesh_terms: D001483:Base Sequence; D052639:Caulimoviridae / Q000235:genetics*; D032461:Chromosomes, Plant / Q000235:genetics; D003001:Cloning, Molecular; D018506:Gene Expression Regulation, Plant; D015967:Gene Expression Regulation, Viral; D018745:Genome, Plant; D017404:In Situ Hybridization, Fluorescence; D018551:Solanum lycopersicum / Q000145:classification / Q000235:genetics* / Q000821:virology*; D008969:Molecular Sequence Data; D010802:Phylogeny; D018626:Retroelements / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D019657:Solanaceae / Q000235:genetics / Q000821:virology; D014026:Nicotiana / Q000235:genetics / Q000821:virology
chemical_list: D018626:Retroelements