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Bacterial Pangenomics

Methods and Protocols

  • Book
  • © 2021

Overview

Editors:
  1. Alessio Mengoni

    1. Department of Biology, University of Florence, Sesto Fiorentino, Italy

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    You can also search for this editor in PubMed   Google Scholar

  2. Giovanni Bacci

    1. Department of Biology, University of Florence, Sesto Fiorentino, Italy

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    You can also search for this editor in PubMed   Google Scholar

  3. Marco Fondi

    1. Department of Biology, University of Florence, Sesto Fiorentino, Italy

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  • Includes cutting-edge techniques
  • Provides step-by-step detail essential for reproducible results
  • Contains key implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 2242)

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Table of contents (16 protocols)

  1. Front Matter

    Pages i-x
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  2. Opportunities from Novel Sequencing Technologies

    1. Front Matter

      Pages 1-1
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    2. PacBio-Based Protocol for Bacterial Genome Assembly

      • Agata Motyka-Pomagruk, Sabina Zoledowska, Michal Kabza, Ewa Lojkowska
      Pages 3-14

    3. The Illumina Sequencing Protocol and the NovaSeq 6000 System

      • Alessandra Modi, Stefania Vai, David Caramelli, Martina Lari
      Pages 15-42

  3. Pangenomics of Cultured Isolates

    1. Front Matter

      Pages 43-43
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    2. Comparative Analysis of Core and Accessory Genes in Coexpression Network

      • Biliang Zhang, Jian Jiao, Pan Zhang, Wen-Jing Cui, Ziding Zhang, Chang-Fu Tian
      Pages 45-58

    3. Inferring Core Genome Phylogenies for Bacteria

      • Alexander Keller, Markus J. Ankenbrand
      Pages 59-68

    4. Inferring Phylogenomic Relationship of Microbes Using Scalable Alignment-Free Methods

      • Guillaume Bernard, Timothy G. Stephens, Raúl A. González-Pech, Cheong Xin Chan
      Pages 69-76

    5. Fast Phylogeny Reconstruction from Genomes of Closely Related Microbes

      • Bernhard Haubold, Fabian Klötzl
      Pages 77-89

    6. Comparative Genomics, from the Annotated Genome to Valuable Biological Information: A Case Study

      • Sabina Zoledowska, Agata Motyka-Pomagruk, Agnieszka Misztak, Ewa Lojkowska
      Pages 91-112

  4. Dark Matter Pangenomics

    1. Front Matter

      Pages 113-113
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    2. Accurate Annotation of Microbial Metagenomic Genes and Identification of Core Sets

      • Chiara Vanni
      Pages 115-138

    3. Metagenomic Assembly: Reconstructing Genomes from Metagenomes

      • Zhang Wang, Jie-Liang Liang, Li-Nan Huang, Alessio Mengoni, Wen-Sheng Shu
      Pages 139-152

    4. Genome Recovery, Functional Profiling, and Taxonomic Classification from Metagenomes

      • Davide Albanese, Claudio Donati
      Pages 153-172

    5. Functional Metagenomics for Identification of Antibiotic Resistance Genes (ARGs)

      • Francesca Di Cesare
      Pages 173-183

    6. Host Trait Prediction from High-Resolution Microbial Features

      • Giovanni Bacci
      Pages 185-202

  5. Progresses in Genome-to-Phenome Inference

    1. Front Matter

      Pages 203-203
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    2. Phylogenetic Methods for Genome-Wide Association Studies in Bacteria

      • Xavier Didelot
      Pages 205-220

    3. Simple, Reliable, and Time-Efficient Manual Annotation of Bacterial Genomes with MAISEN

      • Mikolaj Dziurzynski, Przemyslaw Decewicz, Karol Ciuchcinski, Adrian Gorecki, Lukasz Dziewit
      Pages 221-229

  6. Cookbook for Pangenomics

    1. Front Matter

      Pages 231-231
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Keywords

About this book

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.

Editors and Affiliations

  • Department of Biology, University of Florence, Sesto Fiorentino, Italy

    Alessio Mengoni, Giovanni Bacci, Marco Fondi

Bibliographic Information

  • Book Title: Bacterial Pangenomics

  • Book Subtitle: Methods and Protocols

  • Editors: Alessio Mengoni, Giovanni Bacci, Marco Fondi

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-0716-1099-2

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2021

  • Hardcover ISBN: 978-1-0716-1098-5Published: 07 May 2021

  • Softcover ISBN: 978-1-0716-1101-2Published: 07 May 2022

  • eBook ISBN: 978-1-0716-1099-2Published: 07 May 2021

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 2

  • Number of Pages: X, 268

  • Number of Illustrations: 17 b/w illustrations, 42 illustrations in colour

  • Topics: Microbial Genetics and Genomics, Microbiology, Biological Techniques

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