title: The genome of African yam (Dioscorea cayenensis-rotundata complex) hosts endogenous sequences from four distinct Badnavirus species.
abstract: Several endogenous viral elements (EVEs) have been identified in plant genomes, including endogenous pararetroviruses (EPRVs). Here, we report the first characterization of EPRV sequences in the genome of African yam of the Dioscorea cayenensis-rotundata complex. We propose that these sequences should be termed 'endogenous Dioscorea bacilliform viruses' (eDBVs). Molecular characterization of eDBVs shows that they constitute sequences originating from various parts of badnavirus genomes, resulting in a mosaic structure that is typical of most EPRVs characterized to date. Using complementary molecular approaches, we show that eDBVs belong to at least four distinct Badnavirus species, indicating multiple, independent, endogenization events. Phylogenetic analyses of eDBVs support and enrich the current taxonomy of yam badnaviruses and lead to the characterization of a new Badnavirus species in yam. The impact of eDBVs on diagnosis, yam germplasm conservation and movement, and breeding is discussed.
authors.affiliation: INRA, UR1321 ASTRO Agrosystèmes tropicaux, F-97170, Petit-Bourg, (Guadeloupe), France.
authors.forename: Marie
authors.initials: M
authors.lastname: Umber
authors.forename: Denis
authors.initials: D
authors.lastname: Filloux
authors.forename: Emmanuelle
authors.initials: E
authors.lastname: Muller
authors.forename: Nathalie
authors.initials: N
authors.lastname: Laboureau
authors.forename: Serge
authors.initials: S
authors.lastname: Galzi
authors.forename: Philippe
authors.initials: P
authors.lastname: Roumagnac
authors.forename: Marie-Line
authors.initials: ML
authors.lastname: Iskra-Caruana
authors.forename: Claudie
authors.initials: C
authors.lastname: Pavis
authors.forename: Pierre-Yves
authors.initials: PY
authors.lastname: Teycheney
authors.forename: Susan E
authors.initials: SE
authors.lastname: Seal
mesh_terms: D000349:Africa; D019195:Badnavirus / Q000235:genetics*; D001483:Base Sequence; D015139:Blotting, Southern; D018744:DNA, Plant / Q000235:genetics; D027742:Dioscorea / Q000235:genetics* / Q000821:virology*; D020077:Endogenous Retroviruses / Q000235:genetics; D015321:Gene Rearrangement / Q000235:genetics; D014644:Genetic Variation; D018745:Genome, Plant / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D036226:Seedlings / Q000821:virology
chemical_list: D018744:DNA, Plant
keywords: Dioscorea cayenensis-rotundata complex; badnavirus; endogenous pararetrovirus; phylogeny; yam