title: Network Analysis of Plasmidomes: The Azospirillum brasilense Sp245 Case.
abstract: Azospirillum brasilense is a nitrogen-fixing bacterium living in association with plant roots. The genome of the strain Sp245, isolated in Brazil from wheat roots, consists of one chromosome and six plasmids. In this work, the A. brasilense Sp245 plasmids were analyzed in order to shed some light on the evolutionary pathways they followed over time. To this purpose, a similarity network approach was applied in order to identify the evolutionary relationships among all the A. brasilense plasmids encoded proteins; in this context a computational pipeline specifically devoted to the analysis and the visualization of the network-like evolutionary relationships among different plasmids molecules was developed. This information was supplemented with a detailed (in silico) functional characterization of both the connected (i.e., sharing homology with other sequences in the dataset) and the unconnected (i.e., not sharing homology) components of the network. Furthermore, the most likely source organism for each of the genes encoded by A. brasilense plasmids was checked, allowing the identification of possible trends of gene loss/gain in this microorganism. Data obtained provided a detailed description of the evolutionary landscape of the plasmids of A. brasilense Sp245, suggesting some of the molecular mechanisms responsible for the present-day structure of these molecules.
authors.affiliation: Institute of Protein Biochemistry, National Research Council, Via P. Castellino 111, 80134 Naples, Italy ; Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Firenze, Italy.
authors.forename: Valerio
authors.identifier: 0000-0002-6857-5471
authors.initials: V
authors.lastname: Orlandini
authors.affiliation: Tree and Timber Institute, National Research Council, Via Madonna del Piano 10, 50019 Fiorentino, Firenze, Italy.
authors.forename: Giovanni
authors.identifier: 0000-0002-1264-8002
authors.initials: G
authors.lastname: Emiliani
authors.affiliation: Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Firenze, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Fondi
authors.affiliation: Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Firenze, Italy.
authors.forename: Isabel
authors.identifier: 0000-0002-6304-1964
authors.initials: I
authors.lastname: Maida
authors.affiliation: Laboratory of Microbial and Molecular Evolution, Department of Biology, University of Florence, Via Madonna del Piano 6, 50019 Sesto Fiorentino, Firenze, Italy.
authors.forename: Elena
authors.identifier: 0000-0001-5148-3178
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, 50019 Sesto Fiorentino, Firenze, Italy.
authors.forename: Renato
authors.identifier: 0000-0001-9114-2335
authors.initials: R
authors.lastname: Fani