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Appearances can be deceptive: Revealing a hidden viral infection with deep sequencing in a plant quarantine Context

Candresse Thierry, Filloux Denis, Muhire Brejnev, Julian Charlotte, Galzi Serge, Fort Guillaume, Bernardo Pauline, Daugrois Jean-Heinrich, Fernandez Emmanuel, Martin Darren Patrick, Varsani Arvind, Roumagnac Philippe. 2014. Appearances can be deceptive: Revealing a hidden viral infection with deep sequencing in a plant quarantine Context. PloS One, 9 (7):e102945, 13 p.

Journal article ; Article de revue à facteur d'impact Revue en libre accès total
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Quartile : Q1, Sujet : MULTIDISCIPLINARY SCIENCES

Liste HCERES des revues (en SHS) : oui

Thème(s) HCERES des revues (en SHS) : Psychologie-éthologie-ergonomie; Staps

Abstract : Comprehensive inventories of plant viral diversity are essential for effective quarantine and sanitation efforts. The safety of regulated plant material exchanges presently relies heavily on techniques such as PCR or nucleic acid hybridisation, which are only suited to the detection and characterisation of specific, well characterised pathogens. Here, we demonstrate the utility of sequence-independent next generation sequencing (NGS) of both virus-derived small interfering RNAs (siRNAs) and virion-associated nucleic acids (VANA) for the detailed identification and characterisation of viruses infecting two quarantined sugarcane plants. Both plants originated from Egypt and were known to be infected with Sugarcane streak Egypt Virus (SSEV; Genus Mastrevirus, Family Geminiviridae), but were revealed by the NGS approaches to also be infected by a second highly divergent mastrevirus, here named Sugarcane white streak Virus (SWSV). This novel virus had escaped detection by all routine quarantine detection assays and was found to also be present in sugarcane plants originating from Sudan. Complete SWSV genomes were cloned and sequenced from six plants and all were found to share >91% genome-wide identity. With the exception of two SWSV variants, which potentially express unusually large RepA proteins, the SWSV isolates display genome characteristics very typical to those of all other previously described mastreviruses. An analysis of virus-derived siRNAs for SWSV and SSEV showed them to be strongly influenced by secondary structures within both genomic single stranded DNA and mRNA transcripts. In addition, the distribution of siRNA size frequencies indicates that these mastreviruses are likely subject to both transcriptional and post-transcriptional gene silencing. Our study stresses the potential advantages of NGS-based virus metagenomic screening in a plant quarantine setting and indicates that such techniques could dramatically reduce the numbers of non-intercepted virus pathogens passing through plant quarantine stations. (Résumé d'auteur)

Mots-clés Agrovoc : Saccharum officinarum, quarantaine, Virus des végétaux, Virologie, Séquence nucléotidique, Identification, Analyse qualitative, Géminivirus, Méthodologie

Mots-clés géographiques Agrovoc : Égypte

Mots-clés complémentaires : Séquencage

Classification Agris : H20 - Plant diseases
U30 - Research methods

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

Auteurs et affiliations

  • Candresse Thierry, INRA (FRA)
  • Filloux Denis, CIRAD-BIOS-UMR BGPI (FRA)
  • Muhire Brejnev, UCT (ZAF)
  • Julian Charlotte, INRA (FRA)
  • Galzi Serge, CIRAD-BIOS-UMR BGPI (FRA)
  • Fort Guillaume, INRA (FRA)
  • Bernardo Pauline, CIRAD-BIOS-UMR BGPI (FRA)
  • Daugrois Jean-Heinrich, CIRAD-BIOS-UMR BGPI (FRA)
  • Fernandez Emmanuel, CIRAD-BIOS-UMR BGPI (FRA)
  • Martin Darren Patrick, Institute of Infectious Diseases and Molecular Medicine (ZAF)
  • Varsani Arvind, University of Canterbury (NZL)
  • Roumagnac Philippe, CIRAD-BIOS-UMR BGPI (FRA) ORCID: 0000-0001-5002-6039

Source : Cirad - Agritrop (https://agritrop.cirad.fr/573727/)

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