Bacterial Pangenomics Methods and Protocols

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. 

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, Raúl A. González-Pech, and Cheong Xin Chan

 

6. Fast Phylogeny Reconstruction from Genomes of Closely Related Microbes

            Bernhard Haubold and Fabian Klötzl

 

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