Preface ......................................................... v
Contributors ................................................... ix
1 Pulsed Field Gel Electrophoresis and Genome Size Estimates ... 1
Rosa Alduina and Annalisa Pisciotta
2 Comparative Analyses of Extrachromosomal Bacterial
Replicons, Identification of Chromids, and Experimental
Evaluation of Their Indispensability ........................ 15
Lukasz Dziewit and Dariusz Bartosik
3 Choice of Next-Generation Sequencing Pipelines .............. 31
F. Del Chierico, M. Ancora, M. Marcacci, C. Camma,
L. Putignani, and Salvatore Conti
4 The Pyrosequencing Protocol for Bacterial Genomes ........... 49
Ermanno Rizzi
5 Bacterial Metabarcoding by 16S rRNA Gene Ion Torrent
Amplicon Sequencing ......................................... 77
Elio Fantini, Giulio Gianese, Giovanni Giuliano, and
Alessia Fiore
6 The Illumina-Solexa Sequencing Protocol for Bacterial
Genomes ..................................................... 91
Zhenfei Нu, Lei Cheng, and Hai Wang
7 High-Throughput Phenomics ................................... 99
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 ........ 125
Paolo Sonego, Pieter Meysman, Marco Moretto, Roberto
Viola, Kris Laukens, Duccio Cavalieri, and Kristof
Engelen
9 Raw Sequence Data and Quality Control ...................... 137
Giovanni Bacci
10 Methods for Assembling Reads and Producing Contigs ......... 151
Valerio Orlandini, Marco Fondi, and Renato Fani
11 Mapping Contigs Using CONTIGuator .......................... 163
Marco Galardini, Alessio Mengoni, and Marco Bazzicalupo
12 Gene Calling and Bacterial Genome Annotation with BG7 ...... 177
Raquel Tobes, Pablo Pareja-Tobes, Marina Manrique,
Eduardo Pareja-Tobes, Evdokim Kovach, Alexey Alekhin, and
Eduardo Pareja
13 Defining Orthologs and Pangenome Size Metrics .............. 191
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 .................................. 203
Pablo Vinuesa and Bruno Contreras-Moreira
15 Genome-Scale Metabolic Network Reconstruction .............. 233
Marco Fondi and Pietro Lió
16 From Pangenome to Panphenome and Back ...................... 257
Marco Galardini, Atessio Mengoni, and Stefano Mocali
17 Genome-Wide Detection of Selection and Other Evolutionary
Forces ..................................................... 271
Zhuofei Xu and Rui Zhou
18 The Integrated Microbial Genome Resource of Analysis ....... 289
Alice Checcucci and Alessio Mengoni
Index ......................................................... 297
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