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Research Project: CHARACTERIZING, DETECTING, AND ELIMINATING PATHOGENS TO ENABLE THE SAFE INTRODUCTION OF PLANT GENETIC RESOURCES

Location: National Germplasm Resources Laboratory

Title: Sugarcane mild mosaic virus: towards the full characterization of this sugarcane Ampelovirus re-discovered using metagenomics-based approaches

Author
item Daugrois, Jean-heinrich - Cirad, France
item Candresse, Thierry - Inra, Génétique Animale Et Biologie Intégrative , Jouy-En-josas, France
item Fernandez, Emmanuel - Cirad, France
item Fillouz, Dennis - Cirad, France
item Julian, Charlotte - Cirad, France
item Teycheney, Pierre-yves - Cirad, France
item Mollov, Dimitre
item Roumagnac, Philippe - Cirad, France

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 11/30/2016
Publication Date: 1/15/2017
Citation: Daugrois, J., Candresse, T., Fernandez, E., Fillouz, D., Julian, C., Teycheney, P., Mollov, D.S., Roumagnac, P. 2017. Sugarcane mild mosaic virus: towards the full characterization of this sugarcane Ampelovirus re-discovered using metagenomics-based approaches. Meeting Abstract. 16ièmes Rencontres de Virologie Végétale – 15 – 19 janvier 2017 – Aussois – France. Page 64.

Interpretive Summary:

Technical Abstract: Sugarcane mild mosaic virus (SCMMV) is a closterovirus-like virus that was discovered by Lockhart et al. (1992). SCMMV is provisionally assigned to the genus Ampelovirus, family Closteroviridae (Martelli et al 2002). Since the initial serological and microscopical studies, no new information about SCMMV has been obtained. Recently, without a priori metagenomics-based approaches, including virion-associated nucleic acid (VANA) and siRNAs sequencing were used for the virological screening of sugarcane varieties from sugarcane quarantine and biological resource collections. Metagenomics-based reads were de novo assembled and the obtained contigs were compared to sequences stored in the GenBank by BlastN and BlastX. In addition, the metagenomics-based reads were mapped to known sugarcane viruses and reference genomes of other plant viruses, including ampeloviruses. While the combination of both metagenomics approaches yielded contigs with homologies to large parts of the genome of representative members of the Ampelovirus genus, a whole transcriptome shotgun sequencing approach based on total RNA extracted from SCMMV infected sugarcane variety yielded the largest portion of the novel ampelovirus genome (total assembled scaffold length 12,408nt). Based on nucleotide similarity, the most closely related of the ampeloviruses to the novel amplelovirus contig is Plum bark necrosis stem pitting-associated virus with only 44.4% identity, suggesting, as expected, that the agent identified is a novel ampelovirus. NGS data were also used to design specific detection primers located within the HPS70 gene. Forty-nine sugarcane varieties from the Cirad sugarcane quarantine program tested positive for this ampelovirus using the detection primers, providing a first vision of the prevalence and diversity of this novel virus. Further studies will be needed to definitively confirm using serological approaches that the contemporary ampelovirus is actually the same agent as the initially described SCMMV. Whatever the conclusion on this specific question, the present study sheds light on the diversity and the geographic distribution of an uncharacterized sugarcane ampelovirus. The full molecular characterization of this virus and the confirmation whether or not it is SCMMV is important to set quarantine rules regarding its diagnostics and plant sanitation.