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.

Current status of viroid taxonomy

“…The acronyms refer to extended names of viroids: apple dimple fruit viroid (ADFVd), apple scar skin viroid (ASSVd), Australian grapevine viroid (AGVd), avocado sunblotch viroid (ASBVd), chrysanthemum chlorotic mottle viroid (CChMVd), citrus bark cracking viroid (CBCVd), citrus bent leaf viroid (CBLVd), citrus dwarfing viroid (CDVd), citrus viroid V (CVd V), citrus viroid VI (CVd VI), coconut cadang-cadang viroid (CCCVd), coconut tinangaja viroid (CTiVd), coleus blumei viroid 1 (CbVd-1), coleus blumei viroid 2 (CbVd-2), coleus blumei viroid 3 (CbVd-3), grapevine yellow speckle viroid 1 (GYSVd-1), grapevine yellow speckle viroid 2 (GYSVd-2), eggplant latent viroid (ELVd), hop latent viroid (HLVd), hop stunt viroid (HSVd), peach latent mosaic viroid (PLMVd), pear blister canker viroid (PBCVd). The acronyms of members of the genus Pospiviroid refer to extended names of viroids according to Table 2 Similar to the situation with CLVd, the need to formally consider whether DLVd belongs to a novel species [63] offers an opportunity to revisit this decision in the light of new evidence. DLVd, with less than 56% sequence identity to other viroids, displays characteristic features of members of the family Pospiviroidae, including a predicted rod-like secondary structure of minimum free energy with a CCR identical to that of HSVd (genus Hostuviroid).…”

“…However, DLVd has the TCR present in members of the genus Pospiviroid, but absent in HSVd, and lacks the TCH present in HSVd. Phylogenetic reconstructions indicate that HSVd and pepper chat fruit viroid (PCFVd) (genus Pospiviroid) are the closest relatives of DLVd [63], but DLVd differs from these viroids in its host range, which is restricted to dahlia so far. Therefore, DLVd fulfils the criteria to belong to a novel species of the family Pospiviroidae.…”

“…The adjective ''polythetic'' means that the viruses (or viroids) do not need to exhibit a common core set of biological, genetic or structural properties, but rather that their properties overlap to varying degrees. As discussed below, this definition provides a useful framework in which to consider the classification of columnea latent viroid (CLVd, [31] and dahlia latent viroid, DLVd, [63]), two viroids whose CCRs most closely resemble that of HSVd but also, like PSTVd, contain a TCR (see below).…”

Dahlia latent viroid and Potato spindle tuber viroid in dahlia plants in the UK

“…Dahlia latent viroid (DLVd) (Hostuviroid, Pospiviroidae) is a recently discovered viroid of dahlia (family Asteraceae) (Verhoeven et al, 2013). Surveys in both The Netherlands and Japan found the viroid to be widespread in both field-and pot-grown dahlia.…”

“…Surveys in both The Netherlands and Japan found the viroid to be widespread in both field-and pot-grown dahlia. No other natural host of this viroid has been found and attempts to inoculate the viroid to other plant species have failed (Verhoeven et al, 2013;Tsushima et al, 2015). Potato spindle tuber viroid (PSTVd) (Pospiviroid, Pospiviroidae), is the only viroid to naturally infect cultivated species of potato (Solanum tuberosum) and is a quarantine pest in the European Union.…”