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Viroid quasispecies revealed by deep sequencing.

Joseph R J Brass1, Robert A Owens2, Jaroslav Matoušek3

  • 1a Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf , Düsseldorf , Germany.

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|December 28, 2016
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Summary
This summary is machine-generated.

Viroids are small RNA pathogens that cause plant diseases. This study analyzed Potato spindle tuber viroid (PSTVd) variants, revealing common mutations and an error rate supporting their replication mechanism.

Keywords:
Error ratePospiviroiderror thresholdquasispeciessequence network mappingsequencing errorviroid-specific small RNA

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Area of Science:

  • Plant Pathology
  • Molecular Virology
  • RNA Biology

Background:

  • Viroids are non-coding, single-stranded, circular RNA pathogens replicating autonomously in plants.
  • Viroid replication mechanisms differ between Pospiviroidae (asymmetric rolling-circle) and Avsunviroidae (symmetric rolling-circle).
  • Viroids induce viroid-specific small RNAs (vsRNAs) involved in post-transcriptional gene silencing.

Purpose of the Study:

  • To analyze Potato spindle tuber viroid (PSTVd) variants and their evolution during infection using deep sequencing.
  • To elucidate the quasi-species composition of PSTVd populations.
  • To investigate common mutations and the error rate associated with PSTVd replication.

Main Methods:

  • Deep sequencing of vsRNAs from PSTVd-infected plants.
  • Bioinformatic analysis to identify and characterize PSTVd variants.
  • Calculation of mutation rates and error thresholds.

Main Results:

  • Identification of novel and known replication-competent PSTVd variants.
  • Discovery of common strand-specific mutations across PSTVd variants.
  • Determination of a mean error rate per nucleotide position (< [Formula: see text]), comparable to Avsunviroidae.

Conclusions:

  • The observed error rate is within the threshold for synthesizing longer-than-unit-length replication intermediates.
  • This supports the asymmetric rolling-circle replication mechanism utilized by Pospiviroidae members like PSTVd.
  • Understanding viroid quasi-species evolution is crucial for managing plant diseases caused by these pathogens.