Viral Metagenomics: Methods and Protocols

ISBN-13: 9781071635148 / Angielski

Vitantonio Pantaleo; Laura Miozzi

Spis treści

Preface…

Table of Contents…

Contributing Authors…

1. Exploring the Archaeal Virosphere by Metagenomics

Yifan Zhou, Yongjie Wang, David Prangishvili, and Mart Krupovic

2. From Whole-Genome Shotgun Sequencing to Viral Community Profiling: The ViromeScan Tool

Simone Rampelli, Silvia Turroni, and Marco Candela

3. Freshwater Viral Metagenome Analyses Targeting dsDNA Viruses

Kira Moon and Jang-Choen Cho

4. Discovery and Identification of Viruses Infecting Oomycetes

Anna Poimala and Eeva J. Vainio

5. Metagenomic Analyses of Viruses in the Orchid Mycorrhizal Interaction using Improved Assemble Tools

Kota Kambara, Hanako Shimura, Kaien Fujino, and Chikara Masuta

6. Determination of the Mycovirome of a Necrotrophic Fungus

Ana Ruiz-Padilla, Julio L. Rodríguez-Romero, Davide Pacifico, and María A. Ayllón

7. From Metagenomics to Ecogenomics: NGS-Based Approaches for Discovery of New Circular DNA Single-Stranded Viral Species

Enrique A. Guevara-Rivera, Edgar A. Rodríguez-Negrete, Rosa Lozano-Durán, Eduardo R. Bejarano, Alan M. Torres-Calderón, Ángela P. Arce-Leal, Norma E. Leyva-López, and Jesús Méndez-Lozano

8. SARS-CoV-2 Detection and Genome Sequencing in Urban Wastewaters

Enric Cuevas-Ferrando, Gloria Sánchez, and Alba Pérez-Cataluña

9. Enrichment, Sequencing, and Identification of DNA Bacteriophages from Fecal Samples

Quentin Lamy-Besnier and Julian R. Garneau

10. Exploration and Retrieval of Virus-Related Molecular Data using ExTaxsI: The Monkeypox Use Case

Alberto Brusati, Giulia Agostinetto, Antonia Bruno, Maurizio Casiraghi, Dario Pescini, Anna Sandionigi, and Bachir Balech

11. Optimized Recovery of Viral DNA and RNA from Blood Plasma for Viral Metagenomics

María Cebriá-Mendoza, Wladimiro Díaz, Rafael Sanjuán, and José M. Cuevas

12. Targeted Whole Genome Sequencing of the Capripoxvirus Genome from Clinical Tissue Samples and Lyophilized Vaccine Batches

Elisabeth Mathijs and Frank Vandenbussche

13. Viromes of Plants Determined by High-Throughput Sequencing of Virus Derived siRNAs

Nikoletta Jaska-Czotter, Zsuzanna Nagyne-Galbacs, Almash Jahan, Emese Demian, and Éva Várallyay

14. Validation of High-Throughput Sequencing (HTS) for Routine Detection of Citrus Viruses and Viroids

Rachelle Bester and Hans J. Maree

15. Identification of DNA Viruses in Ancient DNA from Herbarium Samples

Gianluca Grasso, Silvia Rotunno, Régis Debruyne, Lucie Bittner, Laura Miozzi, Roland Marmesse, and Valeria Bianciotto

16. The Oxford Nanopore MinION as a Versatile Technology for the Diagnosis and Characterization of Emerging Plant Viruses

Giulia Tarquini, Simone Maestri, Paolo Ermacora, and Marta Martini

17. Detection of Plant Viruses using Nanopore Sequencing Based Metagenomic Approach

Anja Pecman, Nataša Mehle and Denis Kutnjak

18. Application of Nanopore-Based Sequencing to Identify Virus Infections in Woody Plants

Serafina Serena Amoia, Michela Chiumenti, and Angelantonio Minafra

19. Distribution of Small RNAs Along Transposable Elements in Vitis vinifera during Somatic Embryogenesis

Silvia Rotunno, Paola Leonetti, Gyorgy Szittya, and Vitantonio Pantaleo

Subject Index List…

Blurb

This second edition volume expands on the previous edition with discussions about the latest viral metagenomics aspects covering a range of different specimens such as soil, freshwater, wastewater, fecal samples, blood plasma, clinical tissues, fungi, and herbarium samples. Chapters also look at different viral groups including archaeal viruses, eukaryotic viruses, phages, mycoviruses, and circular DNA viruses. Techniques required for studying the three viral metagenomic steps of samples processing, library construction, and analysis of data are also discussed. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

Authoritative and cutting-edge, Vital Metagenomics: Methods and Protocols, Second Edition is a valuable resource for researchers who are interested in learning more about this important and developing field.