Discovery of Replicating Circular RNAs by RNA-Seq and Computational Algorithms

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Viroids are a unique class of subviral pathogens found in plants, and they are difficult to identify since they are free circular non-coding RNAs and often replicate to low levels in host cells. We previously described the computational algorithm PFOR that discovers viroids by analyzing total small RNAs of the infected plants obtained by next-generation sequencing platforms. However, the algorithm written in PERL language is very slow, and viroid identification depends on the in vivo accumulation of extensively overlapping sets of small RNAs to target viroids. Here we report the development of PFOR2 that adopted parallel programming in the C++ language and was significantly faster than PFOR. We also describe a simple computational program that after incorporation into PFOR2 is capable of identifying viroids from deep sequencing of long RNAs instead of small RNAs. Moreover, we report the identification of Grapevine latent viroid (GLVd) and Apple hammerhead viroid-like RNA by the computational approach. Since our new algorithms do not depend on the analysis of viroid-derived small RNAs produced in vivo, it is possible to discover viroids in a wide range of host species including plants, invertebrates and vertebrates.

Vyšlo v časopise: Discovery of Replicating Circular RNAs by RNA-Seq and Computational Algorithms. PLoS Pathog 10(12): e32767. doi:10.1371/journal.ppat.1004553
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.ppat.1004553

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