title: Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography.
abstract: Soil bacteria that also form mutualistic symbioses in plants encounter two major levels of selection. One occurs during adaptation to and survival in soil, and the other occurs in concert with host plant speciation and adaptation. Actinobacteria from the genus Frankia are facultative symbionts that form N(2)-fixing root nodules on diverse and globally distributed angiosperms in the "actinorhizal" symbioses. Three closely related clades of Frankia sp. strains are recognized; members of each clade infect a subset of plants from among eight angiosperm families. We sequenced the genomes from three strains; their sizes varied from 5.43 Mbp for a narrow host range strain (Frankia sp. strain HFPCcI3) to 7.50 Mbp for a medium host range strain (Frankia alni strain ACN14a) to 9.04 Mbp for a broad host range strain (Frankia sp. strain EAN1pec.) This size divergence is the largest yet reported for such closely related soil bacteria (97.8%-98.9% identity of 16S rRNA genes). The extent of gene deletion, duplication, and acquisition is in concert with the biogeographic history of the symbioses and host plant speciation. Host plant isolation favored genome contraction, whereas host plant diversification favored genome expansion. The results support the idea that major genome expansions as well as reductions can occur in facultative symbiotic soil bacteria as they respond to new environments in the context of their symbioses.
authors.affiliation: Université de Lyon, UMR CNRS, 5557 Ecologie Microbienne, IFR41 Bio Environnement et Santé, Université Lyon I, Villeurbanne 69622 cedex, France. normand@biomserv.univ-lyon1.fr
authors.forename: Philippe
authors.initials: P
authors.lastname: Normand
authors.forename: Pascal
authors.initials: P
authors.lastname: Lapierre
authors.forename: Louis S
authors.initials: LS
authors.lastname: Tisa
authors.forename: Johann Peter
authors.initials: JP
authors.lastname: Gogarten
authors.forename: Nicole
authors.initials: N
authors.lastname: Alloisio
authors.forename: Emilie
authors.initials: E
authors.lastname: Bagnarol
authors.forename: Carla A
authors.initials: CA
authors.lastname: Bassi
authors.forename: Alison M
authors.initials: AM
authors.lastname: Berry
authors.forename: Derek M
authors.initials: DM
authors.lastname: Bickhart
authors.forename: Nathalie
authors.initials: N
authors.lastname: Choisne
authors.forename: Arnaud
authors.initials: A
authors.lastname: Couloux
authors.forename: Benoit
authors.initials: B
authors.lastname: Cournoyer
authors.forename: Stephane
authors.initials: S
authors.lastname: Cruveiller
authors.forename: Vincent
authors.initials: V
authors.lastname: Daubin
authors.forename: Nadia
authors.initials: N
authors.lastname: Demange
authors.forename: Maria Pilar
authors.initials: MP
authors.lastname: Francino
authors.forename: Eugene
authors.initials: E
authors.lastname: Goltsman
authors.forename: Ying
authors.initials: Y
authors.lastname: Huang
authors.forename: Olga R
authors.initials: OR
authors.lastname: Kopp
authors.forename: Laurent
authors.initials: L
authors.lastname: Labarre
authors.forename: Alla
authors.initials: A
authors.lastname: Lapidus
authors.forename: Celine
authors.initials: C
authors.lastname: Lavire
authors.forename: Joelle
authors.initials: J
authors.lastname: Marechal
authors.forename: Michele
authors.initials: M
authors.lastname: Martinez
authors.forename: Juliana E
authors.initials: JE
authors.lastname: Mastronunzio
authors.forename: Beth C
authors.initials: BC
authors.lastname: Mullin
authors.forename: James
authors.initials: J
authors.lastname: Niemann
authors.forename: Pierre
authors.initials: P
authors.lastname: Pujic
authors.forename: Tania
authors.initials: T
authors.lastname: Rawnsley
authors.forename: Zoe
authors.initials: Z
authors.lastname: Rouy
authors.forename: Chantal
authors.initials: C
authors.lastname: Schenowitz
authors.forename: Anita
authors.initials: A
authors.lastname: Sellstedt
authors.forename: Fernando
authors.initials: F
authors.lastname: Tavares
authors.forename: Jeffrey P
authors.initials: JP
authors.lastname: Tomkins
authors.forename: David
authors.initials: D
authors.lastname: Vallenet
authors.forename: Claudio
authors.initials: C
authors.lastname: Valverde
authors.forename: Luis G
authors.initials: LG
authors.lastname: Wall
authors.forename: Ying
authors.initials: Y
authors.lastname: Wang
authors.forename: Claudine
authors.initials: C
authors.lastname: Medigue
authors.forename: David R
authors.initials: DR
authors.lastname: Benson
mesh_terms: D004251:DNA Transposable Elements; D004269:DNA, Bacterial; D019143:Evolution, Molecular; D040161:Frankia / Q000235:genetics*; D017353:Gene Deletion; D020440:Gene Duplication; D016680:Genome, Bacterial; D005843:Geography; D019684:Magnoliopsida / Q000382:microbiology*; D008969:Molecular Sequence Data; D009586:Nitrogen Fixation; D010802:Phylogeny; D018517:Plant Roots / Q000382:microbiology; D039002:Prophages; D017422:Sequence Analysis, DNA; D013559:Symbiosis
chemical_list: D004251:DNA Transposable Elements; D004269:DNA, Bacterial