title: Exploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti.
abstract: BACKGROUND
  Sinorhizobium meliloti is a model system for the studies of symbiotic nitrogen fixation. An extensive polymorphism at the genetic and phenotypic level is present in natural populations of this species, especially in relation with symbiotic promotion of plant growth. AK83 and BL225C are two nodule-isolated strains with diverse symbiotic phenotypes; BL225C is more efficient in promoting growth of the Medicago sativa plants than strain AK83. In order to investigate the genetic determinants of the phenotypic diversification of S. meliloti strains AK83 and BL225C, we sequenced the complete genomes for these two strains.
  
  
  RESULTS
  With sizes of 7.14 Mbp and 6.97 Mbp, respectively, the genomes of AK83 and BL225C are larger than the laboratory strain Rm1021. The core genome of Rm1021, AK83, BL225C strains included 5124 orthologous groups, while the accessory genome was composed by 2700 orthologous groups. While Rm1021 and BL225C have only three replicons (Chromosome, pSymA and pSymB), AK83 has also two plasmids, 260 and 70 Kbp long. We found 65 interesting orthologous groups of genes that were present only in the accessory genome, consequently responsible for phenotypic diversity and putatively involved in plant-bacterium interaction. Notably, the symbiosis inefficient AK83 lacked several genes required for microaerophilic growth inside nodules, while several genes for accessory functions related to competition, plant invasion and bacteroid tropism were identified only in AK83 and BL225C strains. Presence and extent of polymorphism in regulons of transcription factors involved in symbiotic interaction were also analyzed. Our results indicate that regulons are flexible, with a large number of accessory genes, suggesting that regulons polymorphism could also be a key determinant in the variability of symbiotic performances among the analyzed strains.
  
  
  CONCLUSIONS
  In conclusions, the extended comparative genomics approach revealed a variable subset of genes and regulons that may contribute to the symbiotic diversity.
authors.affiliation: Department of Evolutionary Biology, University of Firenze, via Romana 17, I-50125 Firenze, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Galardini
authors.forename: Alessio
authors.initials: A
authors.lastname: Mengoni
authors.forename: Matteo
authors.initials: M
authors.lastname: Brilli
authors.forename: Francesco
authors.initials: F
authors.lastname: Pini
authors.forename: Antonella
authors.initials: A
authors.lastname: Fioravanti
authors.forename: Susan
authors.initials: S
authors.lastname: Lucas
authors.forename: Alla
authors.initials: A
authors.lastname: Lapidus
authors.forename: Jan-Fang
authors.initials: JF
authors.lastname: Cheng
authors.forename: Lynne
authors.initials: L
authors.lastname: Goodwin
authors.forename: Samuel
authors.initials: S
authors.lastname: Pitluck
authors.forename: Miriam
authors.initials: M
authors.lastname: Land
authors.forename: Loren
authors.initials: L
authors.lastname: Hauser
authors.forename: Tanja
authors.initials: T
authors.lastname: Woyke
authors.forename: Natalia
authors.initials: N
authors.lastname: Mikhailova
authors.forename: Natalia
authors.initials: N
authors.lastname: Ivanova
authors.forename: Hajnalka
authors.initials: H
authors.lastname: Daligault
authors.forename: David
authors.initials: D
authors.lastname: Bruce
authors.forename: Chris
authors.initials: C
authors.lastname: Detter
authors.forename: Roxanne
authors.initials: R
authors.lastname: Tapia
authors.forename: Cliff
authors.initials: C
authors.lastname: Han
authors.forename: Hazuki
authors.initials: H
authors.lastname: Teshima
authors.forename: Stefano
authors.initials: S
authors.lastname: Mocali
authors.forename: Marco
authors.initials: M
authors.lastname: Bazzicalupo
authors.forename: Emanuele G
authors.initials: EG
authors.lastname: Biondi
mesh_terms: D005798:Genes, Bacterial / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics; D058977:Molecular Sequence Annotation; D009586:Nitrogen Fixation / Q000235:genetics*; D010641:Phenotype; D018085:Regulon / Q000235:genetics; D016962:Sinorhizobium meliloti / Q000235:genetics* / Q000378:metabolism*; D013045:Species Specificity; D013559:Symbiosis / Q000235:genetics*; D014157:Transcription Factors / Q000378:metabolism
chemical_list: D014157:Transcription Factors