Preface. Bacterial pangenomics

From a pioneering field a decade ago, now bacterial genomics is a mature research interdisciplinary field, which is approached by ecologist, geneticists, bacteriologists, molecular biologists and evolutionary biologists working in medical, industrial and basic science. The high diffusion of bacterial genomics in many different fields has been helped by the low costs of genome and transcriptome sequencing performed by the so-called Next Generation Sequencing (NGS) technologies. Now, the cost of a draft bacterial genome sequence is a as low as few hundreds of Euro (or Dollars). This low cost is allowing many laboratories to perform genome sequencing of virtually every “interesting” bacterial strain they have in hand. In parallel, bioinformatic analysis of the data has grown and the specialized bioinformatician is an obliged professional figure in every laboratory which is interested in genome sequencing. One of the most striking difference of bacterial genomics with respect to the genomics of eukaryotic multicellular organisms is the concept of pangenome, which was introduced in the late 2005 by researchers working on bacterial pathogenic species. The pangenome is defined as a genomic approximation to describe a species’ genome in terms of the sum of core (conserved in all strains) and dispensable (variable among strains) genes. For bacterial species the pangenome concept is particularly relevant since closely related strains usually show large differences in gene content between Consequently, when speaking about bacterial genomics, often people are referring to comparative analysis of bacterial genomes, and then, to what we can call “bacterial pangenomics”. Understanding which genetic components of this large pangenomic variability are functionally, clinically or evolutionary relevant is a challenging task; in fact, a large fraction of the dispensable genome is found to have a poor functional characterization. The availability of powerful and precise analysis tools is therefore of paramount importance. Thanks to the large diffusion of bacterial genome analysis (or bacterial pangenomic studies), the present book is intended to provide the most recent methodologies about the study of bacterial pangenomes. Three major areas are covered, namely the experimental methods for approaching bacterial pangenomics (“Preparing the bacterial pangenome”), the bioinformatic pipelines for analysis and annotation of sequence data (“Defining the pangenome”) and finally the methods for inferring functional and evolutionary features from the pangenome (“Interpreting the pangenome”). In each of these section, researchers from both academia and private leading companies of NGS and bioinformatic analysis (as Beijing Genome Institute, Life Technologies, Era7 Bioinformatics) are providing the most up to date protocols and procedures for bacterial genome analysis, from assessment of genome size and structure to the analysis of raw sequence data and their annotation and biological interpretation in terms of gene activity and metabarcoding diversity and genome evolution. The aim of the present book is then to serve as a “field guide” for both qualified investigators on bacterial genomics who want to update their technical knowledge, and for less experienced researchers who want to start working with bacterial genomics and pangenomics. Additionally, the book could serve to graduate students as a manual of methods used in bacterial pangenomics and as a supplemental textbook in classes of genomics and bioinformatics.