Abstract
With a small, circular and non-protein coding RNA genome, viroids are the smallest infectious agents. They invade plants, which in turn may develop symptoms. Since their discovery about 50 years ago, more than thirty viroids have been reported and classified using as species demarcation less than 90 per cent sequence identity on the overall genome and evidence of biological divergence with respect to the closest related viroids. In the last few years, new viroids have been identified that infect latently their (frequently) woody hosts and have a narrow experimental hosts range, complicating and slowing down studies on their biology. As a consequence, several viroids are still waiting for classification. Moreover, the number of new viroids is expected to increase in the next years due to the use of high-throughput sequencing technologies with diagnostics purposes. Therefore, establishment of reliable species demarcation criteria mainly based on molecular features of viroids is needed. Here, viroid classification is reassessed and a scheme based on pairwise sequence identity matrices is developed. After identifying a threshold pairwise identity score (PWIS) for each viroid genus, to be used as a species demarcation criterion, we show that most of those yet unclassified viroids can be assigned to a known or to a new species, thus limiting the need for additional biological evidence to only a few more complex situations. The advantages of this PWIS-based method are that the proposed identity thresholds for species demarcations are not arbitrarily established and evidence for biological divergence is not mandatory. Importantly, the current classification is not essentially modified. A protocol for a tentative fast classification of new viroids according to the proposed approach is also provided.
Highlights
Viroids are tiny, circular, single-stranded RNAs that, despite their lack of protein-coding capacity, infect higher plants (Flores et al 2015; Adkar-Purushothama and Perreault 2020)
While in the family Avsunviroidae the lowest limit of pairwise sequence identity between variants belonging to the same species could be established at about 73 per cent (Fig. 1A), the situation appeared more complex in the Pospiviroidae, where such a limit was less clear because pairwise identity score (PWIS) between variants of some species overlapped with those of different species in the same genus (Fig. 1B)
With respect to the species demarcation criteria adopted in the current ICTV viroid classification, our proposed alternative based on PWISs and appropriate threshold identity score (TIS) has the advantage of not being dependent on the need of biological divergence between existing and new viroids to create novel viroid species
Summary
Circular, single-stranded RNAs that, despite their lack of protein-coding capacity, infect higher plants (Flores et al 2015; Adkar-Purushothama and Perreault 2020). Structural and biochemical features, viroids have been classified in two families: Pospiviroidae and Avsunviroidae (Di Serio et al 2018a). Members of the family Pospiviroidae replicate in the nucleus, adopt rodlike or quasi rod-like conformations with conserved structural motifs [i.e. the central conserved region (CCR) involved in VC The Author(s) 2021.
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