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 bioinformatic 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.
TOC:
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 Li?
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