Résumé
A viral metagenomics-based study of the viromes of Saccharum species from Florida, Reunion, Guadeloupe, and Cirad's sugarcane quarantine in Montpellier, France, was carried out using the virion-associated nucleic acid (VANA) approach. The goal of this study was to identify known and potentially new sugarcane viruses. This study revealed the presence of a potential new Mastrevirus species infecting Saccharum species in Florida, Guadeloupe and Reunion. Seventeen full genome sequences (2738-2749 nt long) were obtained using either rolling circle amplification followed by enzymatic restriction, or PCR using back-to-back primers, followed by cloning of full length restricted fragment or full length amplicon and Sanger sequencing. Three full genome sequences were obtained from S. barberi (Florida), five from S. officinarum (Florida and Guadeloupe), four from S. spontaneum (Florida) and five from sugarcane hybrids (Guadeloupe). BLASTn and BLASTx comparisons between these 17 genome sequences and all sequences in GenBank resulted in the highest identity score with a recently deposited geminivirus genome isolated from sugarcane in China (KR150789, highest percentage identity = 89%, e-value = 0.0). Based on the distribution of pairwise identity scores yielded by the species demarcation tool (SDTv1.2), and using Mastrevirus species demarcation threshold of >78 %, we propose that all 18 genomic sequences (17 from our study and KR150789 from China) belong to the same species of Mastrevirus. ,Because this novel Mastrevirus species has never been tested in routine quarantine detection assays, it most likely occurs in several countries of Africa, America, Asia and the Caribbean Islands. In order to develop a new molecular diagnostic assay, we designed specific detection primers using the alignment of the 18 full available genomes. This assay will be used to screen the 2016 variety collection of Cirad's sugarcane quarantine for the presence of the new Mastrevirus species. Results of this screening and analysis of the genetic diversity of the produced amplicons will be presented. (Résumé d'auteur)