title: Networking in microbes: conjugative elements and plasmids in the genus Alteromonas.
abstract: To develop evolutionary models for the free living bacterium Alteromonas the genome sequences of isolates of the genus have been extensively analyzed. However, the main genetic exchange drivers in these microbes, conjugative elements (CEs), have not been considered in detail thus far. In this work, CEs have been searched in several complete Alteromonas genomes and their sequence studied to understand their role in the evolution of this genus. Six genomes are reported here for the first time.
  
  
  
  We have found nine different plasmids of sizes ranging from 85 to 600 Kb, most of them were found in a single strain. Networks of gene similarity could be established among six of the plasmids that were also connected with another cluster of plasmids found in Shewanella strains. The cargo genes found in these plasmids included cassettes found before in chromosome flexible genomic islands of Alteromonas strains. We describe also the plasmids pAMCP48-600 and pAMCP49-600, the largest found in Alteromonas thus far (ca. 600 Kb) and containing all the hallmarks to be classified as chromids. We found in them some housekeeping genes and a cluster that code for an exocellular polysaccharide. They could represent the transport vectors for the previously described replacement flexible genomic islands. Integrative and conjugative elements (ICEs) were more common than plasmids and showed similar patterns of variation with cargo genes coding for components of additive flexible genomic islands. A nearly identical ICE was found in A. mediterranea MED64 and Vibrio cholera AHV1003 isolated from a human pathogen, indicating the potential exchange of these genes across phylogenetic distances exceeding the family threshold.
  
  
  
  We have seen evidence of how CEs can be vectors to transfer gene cassettes acquired in the chromosomal flexible genomic islands, both of the additive and replacement kind. These CEs showed evidence of how genetic material is exchanged among members of the same species but also (albeit less frequently) across genus and family barriers. These gradients of exchange frequency are probably one of the main drivers of species origin and maintenance in prokaryotes and also provide these taxa with large genetic diversity.
authors.affiliation: Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Apartado 18, San Juan, 03550, Alicante, Spain.
authors.forename: Mario
authors.initials: M
authors.lastname: López-Pérez
authors.affiliation: Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Apartado 18, San Juan, 03550, Alicante, Spain.
authors.forename: Nieves
authors.initials: N
authors.lastname: Ramon-Marco
authors.affiliation: Evolutionary Genomics Group, Departamento de Producción Vegetal y Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Apartado 18, San Juan, 03550, Alicante, Spain. frvalera@umh.es.
authors.forename: Francisco
authors.identifier: 0000-0002-9809-2059
authors.initials: F
authors.lastname: Rodriguez-Valera
mesh_terms: D020591:Alteromonas / Q000145:classification / Q000235:genetics* / Q000378:metabolism; D001482:Base Composition; D019295:Computational Biology / Q000379:methods; D003227:Conjugation, Genetic; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods; D016366:Open Reading Frames; D010802:Phylogeny; D010957:Plasmids / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D025941:Protein Interaction Mapping; D060066:Protein Interaction Maps; D020543:Proteome; D040901:Proteomics / Q000379:methods
chemical_list: D020543:Proteome
keywords: Alteromonas; Chromid; Conjugative elements; Genomic islands; ICE; Integrative and conjugative elements; Pangenome; Plasmids