Viroids are plant pathogens that consist of a short stretch (a few hundred nucleobases) of highly complementary, circular, single-stranded RNA. Viroid genomes are extremely small in size, ranging from 246 to 467 nucleotides (nt), and consisting of fewer than 10,000 atoms. In comparison, the genome of the smallest known viruses capable of causing an infection by themselves are around 2,000 nucleobases in size. The human pathogen hepatitis D virus is similar to viroids.
Viroid RNA does not code for any protein. Their replication mechanism uses RNA polymerase II, a host cell enzyme normally associated with synthesis of messenger RNA from DNA, which instead catalyzes "rolling circle" synthesis of new RNA using the viroid's RNA as template. Some viroids are ribozymes, having catalytic properties which allow self-cleavage and ligation of unit-size genomes from larger replication intermediates.
The first viroid to be identified was Potato spindle tuber viroid (PSTVd). Some 33 species have been identified.
- Family Pospiviroidae
- Genus Pospiviroid; type species: Potato spindle tuber viroid ; 356-361 nt 
- Genus Pospiviroid; type species: Citrus exocortis ; 368-467 nt 
- Genus Hostuviroid; type species: Hop stunt viroid
- Genus Cocadviroid; type species: Coconut cadang-cadang viroid 246-247 nt
- Genus Apscaviroid; type species: Apple scar skin viroid
- Genus Coleviroid; type species: Coleus blumei viroid 1
- Family Avsunviroidae
Viroids and RNA silencing
There has long been confusion over how viroids are able to induce symptoms in plants without encoding any protein products within their sequences. Evidence now suggests that RNA silencing is involved in the process. First, changes to the viroid genome can dramatically alter its virulence. This reflects the fact that any siRNAs produced would have less complementary base pairing with target messenger RNA. Secondly, siRNAs corresponding to sequences from viroid genomes have been isolated from infected plants. Finally, transgenic expression of the noninfectious hpRNA of potato spindle tuber viroid develops all the corresponding viroid like symptoms.
This evidence indicates that when viroids replicate via a double stranded intermediate RNA, they are targeted by a dicer enzyme and cleaved into siRNAs that are then loaded onto the RNA-induced silencing complex. The viroid siRNAs actually contain sequences capable of complementary base pairing with the plant's own messenger RNAs and induction of degradation or inhibition of translation is what causes the classic viroid symptoms.
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