Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains.
BACKGROUND
Sinorhizobium meliloti is a soil bacterium that forms nitrogen-fixing nodules on the roots of leguminous plants such as alfalfa (Medicago sativa). This species occupies different ecological niches, being present as a free-living soil bacterium and as a symbiont of plant root nodules. The genome of the type strain Rm 1021 contains one chromosome and two megaplasmids for a total genome size of 6 Mb. We applied comparative genomic hybridisation (CGH) on an oligonucleotide microarrays to estimate genetic variation at the genomic level in four natural strains, two isolated from Italian agricultural soil and two from desert soil in the Aral Sea region.


RESULTS
From 4.6 to 5.7 percent of the genes showed a pattern of hybridisation concordant with deletion, nucleotide divergence or ORF duplication when compared to the type strain Rm 1021. A large number of these polymorphisms were confirmed by sequencing and Southern blot. A statistically significant fraction of these variable genes was found on the pSymA megaplasmid and grouped in clusters. These variable genes were found to be mainly transposases or genes with unknown function.


CONCLUSIONS
The obtained results allow to conclude that the symbiosis-required megaplasmid pSymA can be considered the major hot-spot for intra-specific differentiation in S. meliloti.
Giuntini
Elisa
E
Dipartimento di Biologia Animale e Genetica, Università di Firenze, via Romana 17, I-50125 Firenze, Italy.
Mengoni
Alessio
A
De Filippo
Carlotta
C
Cavalieri
Duccio
D
Aubin-Horth
Nadia
N
Landry
Christian R
CR
Becker
Anke
A
Bazzicalupo
Marco
M
D015139:Blotting, Southern; D002874:Chromosome Mapping; D016000:Cluster Analysis; D004269:DNA, Bacterial; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D014644:Genetic Variation; D016678:Genome; D016680:Genome, Bacterial; D008957:Models, Genetic; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D009841:Oligonucleotides / Q000737:chemistry; D016366:Open Reading Frames; D020161:Physical Chromosome Mapping; D010957:Plasmids / Q000378:metabolism*; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic; D017422:Sequence Analysis, DNA; D016962:Sinorhizobium meliloti / Q000235:genetics*; D012988:Soil Microbiology; D013559:Symbiosis
D004269:DNA, Bacterial; D009841:Oligonucleotides