Homology-independent discovery of replicating pathogenic circular RNAs by deep sequencing and a new computational algorithm.

ABSTRACT: A common challenge in pathogen discovery by deep sequencing approaches is to recognize viral or subviral pathogens in samples of diseased tissue that share no significant homology with a known pathogen. Here we report a homology-independent approach for discovering viroids, a distinct class of free circular RNA subviral pathogens that encode no protein and are known to infect plants only. Our approach involves analyzing the sequences of the total small RNAs of the infected plants obtained by deep sequencing with a unique computational algorithm, progressive filtering of overlapping small RNAs (PFOR). Viroid infection triggers production of viroid-derived overlapping siRNAs that cover the entire genome with high densities. PFOR retains viroid-specific siRNAs for genome assembly by progressi

SUBMITTER: Wu Q 

PROVIDER: S-EPMC3309787 | biostudies-literature | 2012 Mar

REPOSITORIES: biostudies-literature