title: Retention of the virus-derived sequences in the nuclear genome of grapevine as a potential pathway to virus resistance.
abstract: BACKGROUND
  Previous studies have revealed a wide-spread occurence of the partial and complete genomes of the reverse-transcribing pararetroviruses in the nuclear genomes of herbaceous plants. Although the absence of the virus-encoded integrases attests to the random and incidental incorporation of the viral sequences, their presence could have functional implications for the virus-host interactions.
  
  
  OBJECTIVE
  Analyses of two nuclear genomes of grapevine revealed multiple events of horizontal gene transfer from pararetroviruses. The approximately 200-800 bp inserts that corresponded to partial ORFs encoding reverse transcriptase apparently derived from unknown or extinct caulimoviruses and tungroviruses, were found in 11 grapevine chromosomes. In contrast to the previous reports, no reliable cases of the inserts derived from the positive-strand RNA viruses were found. Because grapevine is known to be infected by the diverse positive-strand RNA viruses, but not pararetroviruses, we hypothesize that pararetroviral inserts have conferred host resistance to these viruses. Furthermore, we propose that such resistance involves RNA interference-related mechanisms acting via small RNA-mediated methylation of pararetroviral DNAs and/or via degradation of the viral mRNAs.
  
  
  CONCLUSIONS
  The pararetroviral sequences in plant genomes may be maintained due to the benefits of virus resistance to this class of viruses conferred by their presence. Such resistance could be particularly significant for the woody plants that must withstand years- to centuries-long virus assault. Experimental research into the RNA interference pathways involving the integrated pararetroviral inserts is required to test this hypothesis.
  
  
  METHODS
  This article was reviewed by Arcady R. Mushegian, I. King Jordan, and Eugene V. Koonin.
authors: Université de Haute-Alsace, Laboratoire Vigne Biotechnologie et Environement EA 3991, 68000 Colmar, France. christophe.bertsch@uha.fr
authors: Christophe
authors: C
authors: Bertsch
authors: Monique
authors: M
authors: Beuve
authors: Valerian V
authors: VV
authors: Dolja
authors: Marion
authors: M
authors: Wirth
authors: Frédérique
authors: F
authors: Pelsy
authors: Etienne
authors: E
authors: Herrbach
authors: Olivier
authors: O
authors: Lemaire
mesh_terms: D020077:Endogenous Retroviruses / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D007113:Immunity, Innate / Q000235:genetics* / Q000502:physiology; D016366:Open Reading Frames / Q000235:genetics; D010935:Plant Diseases / Q000235:genetics / Q000821:virology; D010942:Plant Viruses / Q000235:genetics*; D030821:Plants, Genetically Modified / Q000235:genetics* / Q000821:virology*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D027843:Vitis / Q000235:genetics* / Q000821:virology*