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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 10: The Use of High-Throughput Sequencing for the Study and Diagnosis of Plant Viruses and Viroids in Pollen
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Chapter title
The Use of High-Throughput Sequencing for the Study and Diagnosis of Plant Viruses and Viroids in Pollen
Chapter number 10
Book title
Viral Metagenomics
Published in
Methods in molecular biology, January 2018
DOI 10.1007/978-1-4939-7683-6_10
Pubmed ID
Book ISBNs
978-1-4939-7682-9, 978-1-4939-7683-6
Authors

Kris De Jonghe, Annelies Haegeman, Yoika Foucart, Martine Maes

Abstract

This protocol details the wet lab preparation, extraction of fruit pollen samples, and analysis of the sequencing data following Illumina NextSeq small and total RNA sequencing. The protocol was developed for virus and viroid detection using NGS sequencing and was based on the results of a comparison between different extraction methods followed by yield, RNA purity, and integrity assessment. Moreover, the advantage of an additional ribosomal (r)RNA depletion step to the total RNA extraction protocol was evaluated. The smallRNA procedure is the preferred method of choice. If the total RNA protocol is chosen, the use of the mirVana kit followed by an rRNA depletion step is the best option. The library preparation and sequencing steps were outsourced. As a final step in the data analysis, the VirusDetect software was used to detect the viruses and viroids in the pollen samples.

Mendeley readers

The data shown below were compiled from readership statistics for 13 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 13 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 3 23%
Student > Ph. D. Student 2 15%
Student > Bachelor 2 15%
Unspecified 1 8%
Lecturer 1 8%
Other 2 15%
Unknown 2 15%
Readers by discipline Count As %
Agricultural and Biological Sciences 5 38%
Biochemistry, Genetics and Molecular Biology 5 38%
Unspecified 1 8%
Unknown 2 15%