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Viral Metagenomics

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Cover of 'Viral Metagenomics'

Table of Contents

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    Book Overview
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    Chapter 1 Host-Associated Bacteriophage Isolation and Preparation for Viral Metagenomics
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    Chapter 2 Small RNA Isolation from Tissues of Grapevine and Woody Plants
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    Chapter 3 Double-Stranded RNA-Enriched Preparations to Identify Viroids by Next-Generation Sequencing
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    Chapter 4 Viral Double-Stranded RNAs (dsRNAs) from Plants: Alternative Nucleic Acid Substrates for High-Throughput Sequencing
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    Chapter 5 Workup of Human Blood Samples for Deep Sequencing of HIV-1 Genomes
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    Chapter 6 Monolith Chromatography as Sample Preparation Step in Virome Studies of Water Samples
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    Chapter 7 Viral Metagenomics Approaches for High-Resolution Screening of Multiplexed Arthropod and Plant Viral Communities
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    Chapter 8 Different Approaches to Discover Mycovirus Associated to Marine Organisms
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    Chapter 9 Use of siRNAs for Diagnosis of Viruses Associated to Woody Plants in Nurseries and Stock Collections
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    Chapter 10 The Use of High-Throughput Sequencing for the Study and Diagnosis of Plant Viruses and Viroids in Pollen
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    Chapter 11 High-Resolution Screening of Viral Communities and Identification of New Pathogens in Fish Using Next-Generation Sequencing
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    Chapter 12 Metagenomic Analyses of the Viruses Detected in Mycorrhizal Fungi and Their Host Orchid
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    Chapter 13 DNA Multiple Sequence Alignment Guided by Protein Domains: The MSA-PAD 2.0 Method
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    Chapter 14 From Whole-Genome Shotgun Sequencing to Viral Community Profiling: The ViromeScan Tool
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    Chapter 15 Shannon Entropy to Evaluate Substitution Rate Variation Among Viral Nucleotide Positions in Datasets of Viral siRNAs
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    Chapter 16 Insect Virus Discovery by Metagenomic and Cell Culture-Based Approaches
Attention for Chapter 3: Double-Stranded RNA-Enriched Preparations to Identify Viroids by Next-Generation Sequencing
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Chapter title
Double-Stranded RNA-Enriched Preparations to Identify Viroids by Next-Generation Sequencing
Chapter number 3
Book title
Viral Metagenomics
Published in
Methods in molecular biology, January 2018
DOI 10.1007/978-1-4939-7683-6_3
Pubmed ID
Book ISBNs
978-1-4939-7682-9, 978-1-4939-7683-6
Authors

Beatriz Navarro, Francesco Di Serio

Abstract

Approaches based on next-generation sequencing (NGS) coupled with bioinformatics tools have been developed for detecting viruses and viroids infecting herbaceous and woody plants. Here we describe a protocol to extract nucleic acids from citrus bark and enrich them in double-stranded RNAs. These preparations can be efficiently used for generating cDNA libraries that, after pair-end sequencing and bioinformatics analyses, allow efficient identification of the viroids infecting the source plant.

Mendeley readers

The data shown below were compiled from readership statistics for 6 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 6 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 2 33%
Student > Bachelor 1 17%
Lecturer 1 17%
Student > Master 1 17%
Unknown 1 17%
Readers by discipline Count As %
Agricultural and Biological Sciences 3 50%
Biochemistry, Genetics and Molecular Biology 2 33%
Unknown 1 17%