title: Dahlia latent viroid: a recombinant new species of the family Pospiviroidae posing intriguing questions about its origin and classification.
abstract: A viroid-like RNA has been detected in two asymptomatic dahlia accessions by return and double PAGE. It appeared smaller than Chrysanthemum stunt viroid and Potato spindle tuber viroid, the two members of the genus Pospiviroid, family Pospiviroidae, reported in this ornamental previously. RT-PCR with primers designed for amplifying all pospiviroids produced no amplicons, but RT-PCR with random primers revealed a 342 nt RNA. The sequence of this RNA was confirmed with specific primers, which additionally revealed its presence in many dahlia cultivars. The RNA was named Dahlia latent viroid (DLVd) because it replicates autonomously, but symptomlessly, in dahlia and shares maximum sequence identity with other viroids of less than 56 %. Furthermore, DLVd displays characteristic features of the family Pospiviroidae: a predicted rod-like secondary structure of minimum free energy with a central conserved region (CCR), and the ability to form the metastable structures hairpins I and II. Its CCR is identical to that of Hop stunt viroid (HSVd, genus Hostuviroid). However, DLVd: (i) has the terminal conserved region present in members of the genus Pospiviroid, but absent in HSVd, and (ii) lacks the terminal conserved hairpin present in HSVd. Phylogenetic reconstructions indicate that HSVd and Pepper chat fruit viroid (genus Pospiviroid) are the closest relatives of DLVd, but DLVd differs from these viroids in its host range, restricted to dahlia so far. Therefore, while DLVd fulfils the criteria to be a novel species of the family Pospiviroidae, its recombinant origin makes assignment to the genera Pospiviroid or Hostuviroid problematic.
authors.affiliation: National Plant Protection Organization, National Reference Centre, P.O. Box 9102, 6700 HC Wageningen, The Netherlands.
authors.forename: Jacobus Th J
authors.initials: JTJ
authors.lastname: Verhoeven
authors.affiliation: Naktuinbouw, P.O. Box 40, 2370 AA Roelofarendsveen, The Netherlands.
authors.forename: Ellis T M
authors.initials: ETM
authors.lastname: Meekes
authors.affiliation: National Plant Protection Organization, National Reference Centre, P.O. Box 9102, 6700 HC Wageningen, The Netherlands.
authors.forename: Johanna W
authors.initials: JW
authors.lastname: Roenhorst
authors.affiliation: Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, Valencia 46022, Spain.
authors.forename: Ricardo
authors.initials: R
authors.lastname: Flores
authors.affiliation: Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Universidad Politécnica de Valencia, Valencia 46022, Spain.
authors.forename: Pedro
authors.initials: P
authors.lastname: Serra
mesh_terms: D016000:Cluster Analysis; D017931:DNA Primers / Q000235:genetics; D031944:Dahlia / Q000821:virology*; D019143:Evolution, Molecular; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics*; D020133:Reverse Transcriptase Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D012689:Sequence Homology, Nucleic Acid; D014772:Viroids / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification* / Q000502:physiology; D014779:Virus Replication
chemical_list: D017931:DNA Primers; D012367:RNA, Viral