Characterisation of plant virus populations by a metagenomic approach : Survey in French sub-antarctic islands

• Main Authors: Marais, Armelle, Faure, Chantal, Couture, Carole, Svanella, Laurence, Hullé, Maurice, Le Romancer, Marc, Candresse, Thierry, T.
• Other Authors: Génomique, développement et pouvoir pathogène (GD2P), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Biologie des organismes et des populations appliquées à la protection des plantes (BIO3P), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, Institut Universitaire Européen de la Mer (IUEM), Institut de Recherche pour le Développement (IRD)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Brest (UBO)-Centre National de la Recherche Scientifique (CNRS)
• Format: Conference Object
• Language: English
• Published: HAL CCSD 2009
• Subjects: METAGENOME VIRAL; GENETIQUE; EVOLUTION VIRALE; [SDV]Life Sciences [q-bio]; Antarctic; Kerguelen; Kerguelen Islands; Antarc*
• Online Access: https://hal.inrae.fr/hal-02754641

National audience Only a few number of metagenomic studies concern plant viruses. However, a global knowledge of viral diversity would be very interesting in terms of ecology and could have important impacts on viral taxonomy and diversity studies and, potentially, on the prediction of emerging plant diseases. As an example, the “Plant Virus Biodiversity and Ecology” (PVDE) project has been initiated to survey the biodiversity of vascular plant viruses in the nature Conservancy’s Tallgrass Prairie Preserve of Oklahoma in USA (Wren et al., 2006). Our purpose is to describe the viral metagenome of the French sub-antarctic islands, especially in the Kerguelen islands. This project is included in the nationally funded EVINCE project “Vulnerability of native communities to invasive insects and climate change in sub-Antarctic islands” The ecosystems of these islands provide a suite of environments and scenarios that give key opportunities to improve our understanding of the consequences of climate change and biological invasions on terrestrial ecosystems. An additional interest is that almost nothing is known on the plant viruses present in such remote ecosystems, with the exception of a single report describing a new member of the Badnavirus genus (Skotnicki et al., 2003). Viral screening was done by two approaches. The first one, opened, consists in the analysis of double-stranded RNA, random cloning, sequencing, and comparison with sequences in databanks. By this approach we have been able to detect in an introduced Tropaeolum majus sample, sequences presenting 34% of identity in amino acids (56% of similarity) with the replicase of Oryza sativa endornavirus. The same approach permitted the identification of a new plant or fungal virus in a native plant of Kerguelen islands (Aceana magellanica). The sequences revealed 50% of identity with the capsid of Black raspberry virus F. The second approach consists in the screening of viruses belonging to known viral genera by polyvalent detection RT-PCR tests. One ...