Bacterial pangenomics : methods and protocols

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書誌事項

Bacterial pangenomics : methods and protocols

edited by Alessio Mengoni, Giovanni Bacci, and Marco Fondi

（Methods in molecular biology / John M. Walker, series editor, 2242）（Springer protocols）

Humana Press, c2021

2nd ed

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注記

Includes bibliographical references and index

内容説明・目次

内容説明

This completely revised edition explores novel discoveries in bacterial genomic research, with a focus on technical and computational improvements as well as methods used for bacterial pangenome analysis, which relies on microbiome studies and metagenomic data. Beginning with up-to-date sequencing methods, the book continues with sections covering methods for deep phylogenetic analysis, the role of metagenomic data in understanding the genomics of the many yet uncultured bacteria, progress in genome-to-phenome inference, as well as computational genomic tools. Written for the highly successful Methods in Molecular Biology series, chapters include the type of practical detail necessary for reproducible results in the lab. Authoritative and up-to-date, Bacterial Pangenomics: Methods and Protocols, Second Edition serves as an ideal guide for both highly qualified investigators in bacterial genomics and for less experienced researchers, including students and teachers, who could use a reference for approaching genomic analysis and genome data.

目次

Part I: Opportunities from Novel Sequencing Technologies 1. PacBio-Based Protocol for Bacterial Genomes Assembly Agata Motyka-Pomagruk, Sabina Zoledowska, Michal Kabza, and Ewa Lojkowska 2. The Illumina Sequencing Protocol and the NovaSeq 6000 System Alessandra Modi, Stefania Vai, David Caramelli, and Martina Lari Part II: Pangenomics of Cultured Isolates 3. Comparative Analysis of Core and Accessory Genes in Co-Expression Network Biliang Zhang, Jian Jiao, Pan Zhang, Wen-Jing Cui, Ziding Zhang, and Chang-Fu Tian 4. Inferring Core Genome Phylogenies for Bacteria Alexander Keller and Markus J. Ankenbrand 5. Inferring Phylogenomic Relationship of Microbes Using Scalable Alignment-Free Methods Guillaume Bernard, Timothy G. Stephens, Raul A. Gonzalez-Pech, and Cheong Xin Chan 6. Fast Phylogeny Reconstruction from Genomes of Closely Related Microbes Bernhard Haubold and Fabian Kloetzl 7. Comparative Genomics, from the Annotated Genome to Valuable Biological Information: A Case Study Sabina Zoledowska, Agata Motyka-Pomagruk, Agnieszka Misztak, and Ewa Lojkowska Part III: Dark Matter Pangenomics 8. Accurate Annotation of Microbial Metagenomic Genes and Identification of Core Sets Chiara Vanni 9. Metagenomic Assembly: Reconstructing Genomes from Metagenomes Zhang Wang, Jieliang Liang, Linan Huang, Alessio Mengoni, and Wensheng Shu 10. Genome Recovery, Functional Profiling, and Taxonomic Classification from Metagenomes Davide Albanese and Claudio Donati 11. Functional Metagenomics for Identification of Antibiotic Resistance Genes (ARGs) Francesca Di Cesare 12. Host Trait Prediction from High-Resolution Microbial Features Giovanni Bacci Part IV: Progresses in Genome-to-Phenome Inference 13. Phylogenetic Methods for Genome-Wide Association Studies in Bacteria Xavier Didelot 14. Simple, Reliable, and Time-Efficient Manual Annotation of Bacterial Genomes with MAISEN Mikolaj Dziurzynski, Przemyslaw Decewicz, Karol Ciuchcinski, Adrian Gorecki, and Lukasz Dziewit Part V: Cookbook for Pangenomics 15. A Compendium of Bioinformatic Tools for Bacterial Pangenomics to Be Used by Wet-Lab Scientists Camilla Fagorzi and Alice Checcucci 16. A Protocol for Teaching Basic Next Generations Sequencing (NGS) Analysis Skills to Undergraduate Students Using Bash and R. Marco Fondi and Giovanni Bacci

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