Characterizing small RNAs in filamentous fungi using the rice blast fungus, Magnaporthe oryzae, as an example

Vidhyavathi Raman, Blake C. Meyers, Ralph A. Dean, Nicole M. Donofrio

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

The goal of this chapter is to provide a framework of sequential steps for small RNA (sRNA) analysis in filamentous fungi. Here, we present protocols for (1) comparative analysis of sRNAs in different conditions, (2) comparisons of sRNA libraries to RNAseq data and (3) identification and analysis of methylguanosine-capped and polyadenylated sRNAs (CPA-sRNAs). This species of small RNA is particularly interesting in Magnaporthe oryzae, as they map to transcription start and end sites of protein-coding genes. While we do not provide specific command lines for scripts, we provide a general framework for steps needed to carry out all three types of analyses, including relevant references, websites and free online tools. Screenshots are provided from our own customized interface using M. oryzae as an example, to assist the reader in visualizing many of the steps.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages53-66
Number of pages14
DOIs
StatePublished - 2018
Externally publishedYes

Publication series

NameMethods in Molecular Biology
Volume1848
ISSN (Print)1064-3745

Bibliographical note

Publisher Copyright:
© 2018, Springer Science+Business Media, LLC, part of Springer Nature.

Keywords

  • CPA-sRNAs
  • Fungus
  • RNAseq
  • Small interfering RNAs
  • sRNAs

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