Main description:

This open access book offers the first comprehensive account of the pan-genome concept and its manifold implications.

The realization that the genetic repertoire of a biological species always encompasses more than the genome of each individual is one of the earliest examples of big data in biology that opened biology to the unbounded. The study of genetic variation observed within a species challenges existing views and has profound consequences for our understanding of the fundamental mechanisms underpinning bacterial biology and evolution. The underlying rationale extends well beyond the initial prokaryotic focus to all kingdoms of life and evolves into similar concepts for metagenomes, phenomes and epigenomes.

The book's respective chapters address a range of topics, from the serendipitous emergence of the pan-genome concept and its impacts on the fields of microbiology, vaccinology and antimicrobial resistance, to the study of microbial communities, bioinformatic applications and mathematical models that tie in with complex systems and economic theory.

Given its scope, the book will appeal to a broad readership interested in population dynamics, evolutionary biology and genomics.

Contents:

Preface
Duccio Medini, Herve Tettelin

Section 1. Genomic diversity and the pan-genome concept

1.1 -The pan-genome: a data-drivendiscovery in biology
Duccio Medini, Claudio Donati, Rino Rappuoli, Herve Tettelin

1.2 -The prokaryotic species concept and challenges
Louis-Marie Bobay

1.3 -Bacterial guide on how to design a diversified gene portfolio
Katherine A. Innamorati, Joshua P. Earl, Surya D. Aggarwal, Garth D. Ehrlich, N. Luisa Hiller

1.4 -A review of pan-genome tools and recent studies
George Vernikos

Section2. Evolutionary biology of pan-genomes

2.1 -Structure and dynamics of bacterial populations: pan-genome ecology
Taj Azarian, I-Ting Huang, William P. Hanage

2.2 -Bacterial microevolution and the pan-genome
Florent Lasalle, Xavier Didelot

2.3 -Pan-genomes and selection: the public goods hypothesis
James O. McInerney, Fiona J. Whelan, Maria Rosa Domingo-Sananes, Alan McNally, Mary J. O'Connell

2.4 -A pan-genomic perspective on the emergence, maintenance and predictability of antibiotic resistance
Stephen Wood, Karen Zhu, DefneSurujon, Federico Rosconi, Juan C. Ortiz-Marquez, Tim van Opijnen

Section 3. Pan-genomics: an open, evolving discipline

3.1 -Metapangenome: at the crossroad of pangenomics and metagenomics
Bing Ma, Michael France, Jacques Ravel

3.2 -Pan-genome flux balance analysis towards pan-phenomes
Charles J. Norsigian, Xin Fang, Bernhard O. Palsson, Jonathan M. Monk

3.3 -Bacterial epigenomics: epigenetics in the age of population genomics
Poyin Chen, D.J. Darwin Bandoy, Bart C. Weimer

3.4 -Eukaryotic pan-genomes
Guy-Franck Richard

3.5 -Computational strategies for eukaryotic pan-genome analyses
Zhiqiang Hu, Chaochun Wei, Zhikang Li