title: A common genomic framework for a diverse assembly of plasmids in the symbiotic nitrogen fixing bacteria.
abstract: This work centres on the genomic comparisons of two closely-related nitrogen-fixing symbiotic bacteria, Rhizobium leguminosarum biovar viciae 3841 and Rhizobium etli CFN42. These strains maintain a stable genomic core that is also common to other rhizobia species plus a very variable and significant accessory component. The chromosomes are highly syntenic, whereas plasmids are related by fewer syntenic blocks and have mosaic structures. The pairs of plasmids p42f-pRL12, p42e-pRL11 and p42b-pRL9 as well large parts of p42c with pRL10 are shown to be similar, whereas the symbiotic plasmids (p42d and pRL10) are structurally unrelated and seem to follow distinct evolutionary paths. Even though purifying selection is acting on the whole genome, the accessory component is evolving more rapidly. This component is constituted largely for proteins for transport of diverse metabolites and elements of external origin. The present analysis allows us to conclude that a heterogeneous and quickly diversifying group of plasmids co-exists in a common genomic framework.
authors.affiliation: The Wellcome Trust Sanger Institute, Hinxton, Cambridge, United Kingdom. lcc@sanger.ac.uk
authors.forename: Lisa C
authors.initials: LC
authors.lastname: Crossman
authors.forename: Santiago
authors.initials: S
authors.lastname: Castillo-Ramírez
authors.forename: Craig
authors.initials: C
authors.lastname: McAnnula
authors.forename: Luis
authors.initials: L
authors.lastname: Lozano
authors.forename: Georgios S
authors.initials: GS
authors.lastname: Vernikos
authors.forename: José L
authors.initials: JL
authors.lastname: Acosta
authors.forename: Zara F
authors.initials: ZF
authors.lastname: Ghazoui
authors.forename: Ismael
authors.initials: I
authors.lastname: Hernández-González
authors.forename: Georgina
authors.initials: G
authors.lastname: Meakin
authors.forename: Alan W
authors.initials: AW
authors.lastname: Walker
authors.forename: Michael F
authors.initials: MF
authors.lastname: Hynes
authors.forename: J Peter W
authors.initials: JP
authors.lastname: Young
authors.forename: J Allan
authors.initials: JA
authors.lastname: Downie
authors.forename: David
authors.initials: D
authors.lastname: Romero
authors.forename: Andrew W B
authors.initials: AW
authors.lastname: Johnston
authors.forename: Guillermo
authors.initials: G
authors.lastname: Dávila
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
authors.forename: Víctor
authors.initials: V
authors.lastname: González
mesh_terms: D019143:Evolution, Molecular; D016680:Genome, Bacterial; D008957:Models, Genetic; D009586:Nitrogen Fixation / Q000235:genetics*; D010802:Phylogeny; D010957:Plasmids / Q000235:genetics* / Q000378:metabolism; D042163:Rhizobium etli / Q000235:genetics*; D016961:Rhizobium leguminosarum / Q000235:genetics*; D013559:Symbiosis / Q000235:genetics*; D026801:Synteny