Bacterial pangenomics : methods and protocols
Author(s)
Bibliographic Information
Bacterial pangenomics : methods and protocols
（Methods in molecular biology / John M. Walker, series editor, 2242）（Springer protocols）
Humana Press, c2021
2nd ed
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Note
Includes bibliographical references and index
Description and Table of Contents
Description
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.
Table of Contents
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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