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PMID: 16283928 Published · epublish English Journal Article Research Support, Non-U.S. Gov't

Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains.

BMC genomics ·Vol. 6 ·2005-11-10 ·Pages 158

Giuntini E, Mengoni A, De Filippo C, Cavalieri D, Aubin-Horth N, Landry CR, Becker A, Bazzicalupo M

Abstract

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. 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. 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.

MeSH Terms
Blotting, Southern Chromosome Mapping Cluster Analysis DNA, Bacterial Gene Expression Regulation, Bacterial Genes, Bacterial Genetic Variation Genome Genome, Bacterial Models, Genetic Nucleic Acid Hybridization Oligonucleotide Array Sequence Analysis Oligonucleotides/chemistry Open Reading Frames Physical Chromosome Mapping Plasmids/metabolism Polymerase Chain Reaction Polymorphism, Genetic Sequence Analysis, DNA Sinorhizobium meliloti/genetics Soil Microbiology Symbiosis
Chemicals
DNA, Bacterial Oligonucleotides
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Giuntini Elisa
Dipartimento di Biologia Animale e Genetica, Università di Firenze, via Romana 17, I-50125 Firenze, Italy.
Mengoni Alessio
De Filippo Carlotta
Cavalieri Duccio
Aubin-Horth Nadia
Landry Christian R
Becker Anke
Bazzicalupo Marco
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Article Info
Journal
BMC genomics
Abbr.
BMC Genomics
ISSN
1471-2164
DOI
10.1186/1471-2164-6-158
Published
2005-11-10
Epub
2005-00-10
Pages
158
Language
English
Region
England
NLM ID
100965258
PMCID
PMC1298293
Subset
IM
External Links
PubMed source DOI: 10.1186/1471-2164-6-158 PMC Full Text View journal details
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