Viroid quasispecies revealed by deep sequencing

Result code in IS VaVaI

<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F60077344%3A_____%2F17%3A00480595" target="_blank" >RIV/60077344:_____/17:00480595 - isvavai.cz</a>

Result on the web

<a href="http://dx.doi.org/10.1080/15476286.2016.1272745" target="_blank" >http://dx.doi.org/10.1080/15476286.2016.1272745</a>

DOI - Digital Object Identifier

<a href="http://dx.doi.org/10.1080/15476286.2016.1272745" target="_blank" >10.1080/15476286.2016.1272745</a>

Result language

angličtina

Original language name

Viroid quasispecies revealed by deep sequencing

Original language description

Viroids are non-coding single-stranded circular RNA molecules that replicate autonomously in infected host plants causing mild to lethal symptoms. Their genomes contain about 250-400 nucleotides, depending on viroid species. Members of the family Pospiviroidae, like the Potato spindle tuber viroid (PSTVd), replicate via an asymmetric rolling-circle mechanism using the host DNA-dependent RNA-Polymerase II in the nucleus, while members of Avsunviroidae are replicated in a symmetric rolling-circle mechanism probably by the nuclear-encoded polymerase in chloroplasts. Viroids induce the production of viroid-specific small RNAs (vsRNA) that can direct (post-)transcriptional gene silencing against host transcripts or genomic sequences. Here, we used deep-sequencing to analyze vsRNAs from plants infected with different PSTVd variants to elucidate the PSTVd quasipecies evolved during infection. We recovered several novel as well as previously known PSTVd variants that were obviously competent in replication and identified common strand-specific mutations. The calculated mean error rate per nucleotide position was less than 5 x 10(-3), quite comparable to the value of 2: 5 x 10(-3) reported for a member of Avsunviroidae. The resulting error threshold allows the synthesis of longer-than-unit-length replication intermediates as required by the asymmetric rolling-circle mechanism of members of Pospiviroidae.

Czech name

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Czech description

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Type

J_imp - Article in a specialist periodical, which is included in the Web of Science database

CEP classification

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OECD FORD branch

10608 - Biochemistry and molecular biology

Project

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Continuities

I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace

Publication year

2017

Confidentiality

S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

Name of the periodical

RNA biology

ISSN

1547-6286

e-ISSN

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Volume of the periodical

14

Issue of the periodical within the volume

3

Country of publishing house

US - UNITED STATES

Number of pages

9

Pages from-to

317-325

UT code for WoS article

000396830700007

EID of the result in the Scopus database

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