Résumé
Yams (Dioscorea spp.) are important staple food worldwide, particularly in West Africa and the South Pacific, and also in the Caribbean. Badnaviruses (family Caulimoviridae) are studied extensively due to their high prevalence and economic impact on important tropical crops such as cocoa, banana, sugarcane, citrus and yams, and to their high molecular diversity [1]. Until recently, Dioscorea bacilliform AL virus (DBALV) and Dioscorea bacilliform SN virus (DBSNV) are the only yam-infecting badnaviruses whose genomes have been entirely sequenced [2, 3]. DBALV and DBSNV sequences were used for phylogenetic studies, together with partial nucleotide sequences generated by PCR using badnavirus-specific. These analyses unveiled the existence of 12 distinct badnavirus groups of species in yams [4, 5]. However, three additional species and four new episomal genomes have been characterized by three recent and independent studies. The use of the RCA (Rolling Circle Amplification) to distinguish episomal and endogenous badnaviral sequences highlighted that African yams (complex of species Dioscorea cayenensis-rotundata) were infected by three new Badnavirus species which were never been identified yet, belonging to groups 13, 14 and 15 [6]. Two of them have been fully sequenced and called DBRTV1 (Dioscorea bacilliform rotundata virus 1; group 13) and DBRTV2 (Dioscorea bacilliform rotundata virus 2; group 14). At the same time, a badnavirus prevalence study of the yam collection in the French West Indies Biological Resources Centre for Tropical Plants (BRC-TP) showed that America yams (D.trifida) were infected by only two distinct species from groups 8 and 9 [7]. This study used immunocapture-PCR (IC-PCR) to avoid false positive due to endogenous badnaviral sequences. Nucleotide sequences from group 9 were only reported as endogenous forms in D. cayenensis-rotundata genomes, so this species has been sequenced and called DBTRV (Dioscorea bacilliform trifida virus). Furthermore, in silico analyses of shotgun sequences from a D.alata genome displayed a complete badnavirus genome from group 15, showing that this plant was likely infected by a new uncharacterized species unveil however by RCA. Thus, three different approaches have led to the characterization of four new episomal sequences of yam badnavirus and pointed out that yams from different geographical areas were infected by distinct Badnavirus species. Moreover, the absence of DBTRV-infected plants among D. cayenensis-rotundata accessions studied in two first studies could be explained by the presence of eDBV9 sequences in these yam species that could trigger silencing-based resistance against DBTRV. (Résumé d'auteur)