Bacterial Pangenomics Methods and Protocols

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.

1. Pulsed Field Gel Electrophoresis and Genome Size Estimates

            Rosa Alduina and Annalisa Pisctiotta

2. Comparative Analyses of Extrachromosomal Bacterial Replicons, Identification of Chromids and Experimental Evaluation of their Indispensability

            Lukasz Dziewit and Dariusz Bartosik

3. Choice of Next Generation Sequencin Pipelines

            Federica Del Chierico, Massimo Ancora, Maurilia Marcacci, Cesare Cammà, Lorenza Putignani, and Salvatore Conti

4. The Pyrosequencing Protocol for Bacterial Genomes

            Ermanno Rizzi

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

            Elio Fantini, Giulio Gianese, Giovanni Giuliano, and Alessia Fiore

6. The Ilumina-Solexa Sequencing Protocol for Bacterial Genomes

            Zhenfei Hu, Lei Cheng, and Hai Wang

7. High-Throughput Phenomics         

            Carlo, Viti, Francesca Decorosi, Emmanuela Marchi, Marco Galardini, and Luciana Giovannetti

8. 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, and Kristof Engelen

9. Raw Sequence Data and Quality Control

            Giovanni Bacci

10. Methods for Assembling Reads and Producing Contigs

            Valerio Orlandini, Marco Fondi, and Renato Fani

11. Mapping Contigs Using CONTIGuator

            Marco Galardini, Alessio Mengoni, and Marco Bazzicalup

12. Gene Calling and Bacterial Genome Annotation with BG7

            Raquel Tobes, Pablo Pareja-Tobes, Marina Manrique, Eduardo Pareja-Tobes, Evdokim Kovach, Alexey Alekhin, and Eduardo Pareja

13. Defining Orthologs and Pangenome Size Metrics

            Emanuele Bosi, Renato Fani, and Marco Fondi

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

            Pablo Vinuesa and Bruno Contreras-Moreira

15. Genome-Scale Metabolic Networks Reconstruction

            Marco Fondi and Pietro Liò

16. From Pangenome to Phanphenome and Back

            Marco Galardini, Alessio Mengoni, and Stefano Mocali

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

            Zhuofei Xu and Rui Zhou

18. The Integrated Microbial Genome Resource of Analysis

            Alice Checcucci and Alessio Mengoni