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Computational Workflow for Small RNA Profiling in Virus-Infected Plants.

Livia Donaire1, César Llave2

  • 1Departamento de Biología del Estrés y Patología Vegetal, Centro de Edafología y Biología Aplicada del Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Murcia, Spain.

Methods in Molecular Biology (Clifton, N.J.)
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Summary

This chapter details computational pipelines for analyzing plant viral small RNAs (sRNA) and host responses. It offers cost-efficient methods for next-generation sequencing data mining, requiring basic Unix knowledge.

Keywords:
Antiviral silencingBioinformatic analysisNext generation sequencingPlant virusesSmall RNAssRNA-seq

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Area of Science:

  • Plant Virology
  • Bioinformatics
  • Molecular Biology

Background:

  • Viral infections in plants elicit complex small RNA (sRNA) responses.
  • Understanding these sRNA populations is crucial for plant disease diagnostics and management.
  • Existing computational tools may not fully address the analysis of both viral and host sRNAs during infection.

Purpose of the Study:

  • To present a comprehensive computational workflow for analyzing small RNA (sRNA) populations in virus-infected plants.
  • To provide pipelines for investigating viral sRNAs from known and novel viruses.
  • To offer a method for examining host endogenous sRNAs modulated by viral infections.

Main Methods:

  • Development of in silico computational pipelines for sRNA analysis.
  • Focus on next-generation sequencing (NGS) library preparation and processing.
  • Utilization of free bioinformatics tools and in-house Perl scripts for data mining.

Main Results:

  • A structured workflow for analyzing viral and host sRNAs in infected plants.
  • Guidance on cost-efficient RNA extraction, library preparation, and sequencing.
  • Customizable data mining capabilities using provided scripts and tools.

Conclusions:

  • The described pipelines facilitate efficient in silico analysis of plant viral sRNA data.
  • The workflow supports the identification of viral and host sRNAs, aiding in understanding plant-virus interactions.
  • Accessible tools and methods are provided for researchers with basic Unix command-line experience.