The genomes of many yam species contain transcriptionally active endogenous geminiviral sequences that may be functionally expressed

Filloux Denis, Murrell Sasha, Koohapitagtam M., Golden Michael, Julian Charlotte, Galzi Serge, Uzest Marilyne, Rodier-Goud Marguerite, D'Hont Angélique, Vernerey Marie-Stéphanie, Wilkin P., Peterschmitt Michel, Winter Stephan, Murrell Ben, Martin Darren Patrick, Roumagnac Philippe. 2015. The genomes of many yam species contain transcriptionally active endogenous geminiviral sequences that may be functionally expressed. Virus Evolution, 1 (1), 17 p.

Journal article ; Article de revue à comité de lecture
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Additional Information : Jeux de données enregistrés dans la base GenBank du numéro d'accès KJ629184 au KJ629216, KJ629217 au KJ629236, KJ629237 au KJ629250, KJ629251 au KJ629264, KJ629265 au KJ629274, KJ629275 au KJ629281, KJ629282 au KJ629285.

Abstract : Endogenous viral sequences are essentially 'fossil records' that can sometimes reveal the genomic features of long extinct virus species. Although numerous known instances exist of single-stranded DNA (ssDNA) genomes becoming stably integrated within the genomes of bacteria and animals, there remain very few examples of such integration events in plants. The best studied of these events are those which yielded the geminivirus-related DNA elements found within the nuclear genomes of various Nicotiana species. Although other ssDNA virus-like sequences are included within the draft genomes of various plant species, it is not entirely certain that these are not contaminants. The Nicotiana geminivirus-related DNA elements therefore remain the only definitively proven instances of endogenous plant ssDNA virus sequences. Here, we characterize two new classes of endogenous plant virus sequence that are also apparently derived from ancient geminiviruses in the genus Begomovirus. These two endogenous geminivirus-like elements (EGV1 and EGV2) are present in the Dioscorea spp. of the Enantiophyllum clade. We used fluorescence in situ hybridization to confirm that the EGV1 sequences are integrated in the D. alata genome and showed that one or two ancestral EGV sequences likely became integrated more than 1.4 million years ago during or before the diversification of the Asian and African Enantiophyllum Dioscorea spp. Unexpectedly, we found evidence of natural selection actively favouring the maintenance of EGV-expressed replication-associated protein (Rep) amino acid sequences, which clearly indicates that functional EGV Rep proteins were probably expressed for prolonged periods following endogenization. Further, the detection in D. alata of EGV gene transcripts, small 21–24 nt RNAs that are apparently derived from these transcripts, and expressed Rep proteins, provides evidence that some EGV genes are possibly still functionally expressed in at least some of the Enantiophyllum clade species. (Résumé d'auteur)

Mots-clés Agrovoc : Virus des végétaux, Dioscorea, Amélioration des plantes, Génome, Géminivirus, Séquence nucléotidique, Transcription d'ADN, Expression des gènes, ADN, Virologie, Selection naturelle

Mots-clés géographiques Agrovoc : France

Mots-clés complémentaires : Endovirus

Classification Agris : H20 - Plant diseases
F30 - Plant genetics and breeding

Champ stratégique Cirad : Axe 4 (2014-2018) - Santé des animaux et des plantes

Auteurs et affiliations

  • Filloux Denis, CIRAD-BIOS-UMR BGPI (FRA)
  • Murrell Sasha, UCT (ZAF)
  • Koohapitagtam M., Prince of Songkla University (THA)
  • Golden Michael, Institute of Infectious Diseases and Molecular Medicine (ZAF)
  • Julian Charlotte, CIRAD-BIOS-UMR BGPI (FRA)
  • Galzi Serge, CIRAD-BIOS-UMR BGPI (FRA)
  • Uzest Marilyne, INRA (FRA)
  • Rodier-Goud Marguerite, CIRAD-DG-EVALUATION (FRA)
  • D'Hont Angélique, CIRAD-BIOS-UMR AGAP (FRA)
  • Vernerey Marie-Stéphanie, INRA (FRA)
  • Wilkin P., Royal Botanic Gardens (GBR)
  • Peterschmitt Michel, CIRAD-BIOS-UMR BGPI (FRA)
  • Winter Stephan, Leibniz Institute DSMZ (DEU)
  • Murrell Ben, UCR (USA)
  • Martin Darren Patrick, Institute of Infectious Diseases and Molecular Medicine (ZAF)
  • Roumagnac Philippe, CIRAD-BIOS-UMR BGPI (ZAF) ORCID: 0000-0001-5002-6039

Source : Cirad-Agritrop (

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