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Bacterial Pangenomics

Methods and Protocols

  • Book
  • © 2015

Overview

Editors:
  1. Alessio Mengoni

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

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  2. Marco Galardini

    1. EMBL-EBI, Cambridge, United Kingdom

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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, Florence, Italy

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

Part of the book series: Methods in Molecular Biology (MIMB, volume 1231)

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Table of contents (19 protocols)

  1. Front Matter

    Pages i-x
    Download chapter PDF

  2. Pulsed Field Gel Electrophoresis and Genome Size Estimates

    • Rosa Alduina, Annalisa Pisciotta
    Pages 1-14

  3. Comparative Analyses of Extrachromosomal Bacterial Replicons, Identification of Chromids, and Experimental Evaluation of Their Indispensability

    • Lukasz Dziewit, Dariusz Bartosik
    Pages 15-29

  4. Choice of Next-Generation Sequencing Pipelines

    • F. Del Chierico, M. Ancora, M. Marcacci, C. Cammà, L. Putignani, Salvatore Conti
    Pages 31-47

  5. The Pyrosequencing Protocol for Bacterial Genomes

    • Ermanno Rizzi
    Pages 49-75

  6. Bacterial Metabarcoding by 16S rRNA Gene Ion Torrent Amplicon Sequencing

    • Elio Fantini, Giulio Gianese, Giovanni Giuliano, Alessia Fiore
    Pages 77-90

  7. The Illumina-Solexa Sequencing Protocol for Bacterial Genomes

    • Zhenfei Hu, Lei Cheng, Hai Wang
    Pages 91-97

  8. High-Throughput Phenomics

    • Carlo Viti, Francesca Decorosi, Emmanuela Marchi, Marco Galardini, Luciana Giovannetti
    Pages 99-123

  9. Comparative Analysis of Gene Expression: Uncovering Expression Conservation and Divergence Between Salmonella enterica Serovar Typhimurium Strains LT2 and 14028S

    • Paolo Sonego, Pieter Meysman, Marco Moretto, Roberto Viola, Kris Laukens, Duccio Cavalieri et al.
    Pages 125-135

  10. Raw Sequence Data and Quality Control

    • Giovanni Bacci
    Pages 137-149

  11. Methods for Assembling Reads and Producing Contigs

    • Valerio Orlandini, Marco Fondi, Renato Fani
    Pages 151-161

  12. Mapping Contigs Using CONTIGuator

    • Marco Galardini, Alessio Mengoni, Marco Bazzicalupo
    Pages 163-176

  13. Gene Calling and Bacterial Genome Annotation with BG7

    • Raquel Tobes, Pablo Pareja-Tobes, Marina Manrique, Eduardo Pareja-Tobes, Evdokim Kovach, Alexey Alekhin et al.
    Pages 177-189

  14. Defining Orthologs and Pangenome Size Metrics

    • Emanuele Bosi, Renato Fani, Marco Fondi
    Pages 191-202

  15. Robust Identification of Orthologues and Paralogues for Microbial Pan-Genomics Using GET_HOMOLOGUES: A Case Study of pIncA/C Plasmids

    • Pablo Vinuesa, Bruno Contreras-Moreira
    Pages 203-232

  16. Genome-Scale Metabolic Network Reconstruction

    • Marco Fondi, Pietro Liò
    Pages 233-256

  17. From Pangenome to Panphenome and Back

    • Marco Galardini, Alessio Mengoni, Stefano Mocali
    Pages 257-270

  18. Genome-Wide Detection of Selection and Other Evolutionary Forces

    • Zhuofei Xu, Rui Zhou
    Pages 271-287

  19. The Integrated Microbial Genome Resource of Analysis

    • Alice Checcucci, Alessio Mengoni
    Pages 289-295

  20. Erratum to: Genome-Wide Detection of Selection and Other Evolutionary Forces

    • Zhuofei Xu, Rui Zhou
    Pages E1-E1
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Keywords

About this book

Bacterial genomics is a mature research interdisciplinary field, which is approached by ecologists, geneticists, bacteriologists, molecular biologists and evolutionary biologists working in medical, industrial and basic science. Thanks to the large diffusion of bacterial genome analysis, Bacterial Pangenomics: Methods and Protocols is able to provide the most recent methodologies about the study of bacterial pangenomes by covering the three major areas: the experimental methods for approaching bacterial pangenomics, the bio informatic pipelines for analysis and annotation of sequence data and finally the methods for inferring functional and evolutionary features from the pangenome. Written in the 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 protocols and notes on troubleshooting and avoiding known pitfalls.

Authoritative and easily accessible, Bacterial Pangenomics: Methods and Protocols will serve as a field guide for both qualified bacterial genomics investigators who want to update their technical knowledge, for less experienced researchers who want to start working with bacterial genomics and pangenomics, as well as serving as a manual and supplemental textbook for graduate students of genomics and bioinformatics.

Editors and Affiliations

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

    Alessio Mengoni, Marco Fondi

  • EMBL-EBI, Cambridge, United Kingdom

    Marco Galardini

Bibliographic Information

  • Book Title: Bacterial Pangenomics

  • Book Subtitle: Methods and Protocols

  • Editors: Alessio Mengoni, Marco Galardini, Marco Fondi

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-1720-4

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media New York 2015

  • Hardcover ISBN: 978-1-4939-1719-8Published: 24 October 2014

  • Softcover ISBN: 978-1-4939-5547-3Published: 23 August 2016

  • eBook ISBN: 978-1-4939-1720-4Published: 24 October 2014

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: X, 298

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

  • Topics: Microbiology, Bacteriology, Genetic Engineering

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