title: The pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights.
abstract: Pseudoalteromonas is a genus of ubiquitous marine bacteria used as model organisms to study the biological mechanisms involved in the adaptation to cold conditions. A remarkable feature shared by these bacteria is their ability to produce secondary metabolites with a strong antimicrobial and antitumor activity. Despite their biotechnological relevance, representatives of this genus are still lacking (with few exceptions) an extensive genomic characterization, including features involved in the evolution of secondary metabolites production. Indeed, biotechnological applications would greatly benefit from such analysis.
  
  
  
  Here, we analyzed the genomes of 38 strains belonging to different Pseudoalteromonas species and isolated from diverse ecological niches, including extreme ones (i.e. Antarctica). These sequences were used to reconstruct the largest Pseudoalteromonas pangenome computed so far, including also the two main groups of Pseudoalteromonas strains (pigmented and not pigmented strains). The downstream analyses were conducted to describe the genomic diversity, both at genus and group levels. This allowed highlighting a remarkable genomic heterogeneity, even for closely related strains. We drafted all the main evolutionary steps that led to the current structure and gene content of Pseudoalteromonas representatives. These, most likely, included an extensive genome reduction and a strong contribution of Horizontal Gene Transfer (HGT), which affected biotechnologically relevant gene sets and occurred in a strain-specific fashion. Furthermore, this study also identified the genomic determinants related to some of the most interesting features of the Pseudoalteromonas representatives, such as the production of secondary metabolites, the adaptation to cold temperatures and the resistance to abiotic compounds.
  
  
  
  This study poses the bases for a comprehensive understanding of the evolutionary trajectories followed in time by this peculiar bacterial genus and for a focused exploitation of their biotechnological potential.
authors.affiliation: Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, I-501019, Sesto F.no Florence, Italy.
authors.forename: Emanuele
authors.initials: E
authors.lastname: Bosi
authors.affiliation: Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, I-501019, Sesto F.no Florence, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Fondi
authors.affiliation: Department of Clinical and Experimental Biomedical Science "Mario Serio", University of Florence, Viale Pieraccini, 6, I-50139, Florence, Italy.
authors.forename: Valerio
authors.initials: V
authors.lastname: Orlandini
authors.affiliation: Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, I-501019, Sesto F.no Florence, Italy.
authors.forename: Elena
authors.initials: E
authors.lastname: Perrin
authors.affiliation: Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, I-501019, Sesto F.no Florence, Italy.
authors.forename: Isabel
authors.initials: I
authors.lastname: Maida
authors.affiliation: Institute of Protein Biochemistry, National Research Council, Via Pietro Castellino, 111, I-80131, Naples, Italy.
authors.forename: Donatella
authors.initials: D
authors.lastname: de Pascale
authors.affiliation: Dipartimento di Scienze Chimiche, Complesso Universitario Monte S. Angelo, Via Cintia, I-80126, Naples, Italy.
authors.forename: Maria Luisa
authors.initials: ML
authors.lastname: Tutino
authors.affiliation: Dipartimento di Scienze Chimiche, Complesso Universitario Monte S. Angelo, Via Cintia, I-80126, Naples, Italy.
authors.forename: Ermenegilda
authors.initials: E
authors.lastname: Parrilli
authors.affiliation: Institute for the Coastal Marine Environment, National Research Council, Spianata San Raineri 86, I-98122, Messina, Italy.|Department of Biological and Environmental Sciences, University of Messina, Viale Ferdinando Stagno d'Alcontres 31, I-98166, Messina, Italy.
authors.forename: Angelina
authors.initials: A
authors.lastname: Lo Giudice
authors.affiliation: Department of Life Sciences, Imperial College London, MRC Centre for Molecular Bacteriology and Infection, Flowers Building, 1st floor, South Kensington Campus, London, SW7 2AZ, United Kingdom.
authors.forename: Alain
authors.initials: A
authors.lastname: Filloux
authors.affiliation: Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, I-501019, Sesto F.no Florence, Italy. renato.fani@unifi.it.
authors.forename: Renato
authors.identifier: 0000-0001-9114-2335
authors.initials: R
authors.lastname: Fani
mesh_terms: D000864:Antarctic Regions; D000900:Anti-Bacterial Agents / Q000378:metabolism; D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D003080:Cold Temperature; D030541:Databases, Genetic; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D026901:Membrane Transport Proteins / Q000235:genetics / Q000378:metabolism; D010802:Phylogeny; D031161:Pseudoalteromonas / Q000145:classification / Q000235:genetics*; D064210:Secondary Metabolism / Q000235:genetics
chemical_list: D000900:Anti-Bacterial Agents; D001426:Bacterial Proteins; D026901:Membrane Transport Proteins; C077188:cold-shock protein CspB, Bacteria
keywords: Antarctic bacteria; Antibiotics; Comparative genomics; Horizontal gene transfer; Marine bacteria; Microbial evolution; Pangenome; Pseudoalteromonas