Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of <it>Sinorhizobium meliloti </it>natural strains
<p>Abstract</p> <p>Background</p> <p><it>Sinorhizobium meliloti </it>is a soil bacterium that forms nitrogen-fixing nodules on the roots of leguminous plants such as alfalfa (<it>Medicago sativa</it>). This species occupies different ecological n...
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BMC
2005-11-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/6/158 |
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| author | Landry Christian R Aubin-Horth Nadia Cavalieri Duccio De Filippo Carlotta Mengoni Alessio Giuntini Elisa Becker Anke Bazzicalupo Marco |
| author_facet | Landry Christian R Aubin-Horth Nadia Cavalieri Duccio De Filippo Carlotta Mengoni Alessio Giuntini Elisa Becker Anke Bazzicalupo Marco |
| author_sort | Landry Christian R |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p><it>Sinorhizobium meliloti </it>is a soil bacterium that forms nitrogen-fixing nodules on the roots of leguminous plants such as alfalfa (<it>Medicago sativa</it>). 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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>The obtained results allow to conclude that the symbiosis-required megaplasmid pSymA can be considered the major hot-spot for intra-specific differentiation in <it>S. meliloti</it>.</p> |
| first_indexed | 2024-12-11T03:37:07Z |
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| id | doaj.art-d5d9dc9271c84678a9f1c823d0460cf4 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-11T03:37:07Z |
| publishDate | 2005-11-01 |
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| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-d5d9dc9271c84678a9f1c823d0460cf42022-12-22T01:22:14ZengBMCBMC Genomics1471-21642005-11-016115810.1186/1471-2164-6-158Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of <it>Sinorhizobium meliloti </it>natural strainsLandry Christian RAubin-Horth NadiaCavalieri DuccioDe Filippo CarlottaMengoni AlessioGiuntini ElisaBecker AnkeBazzicalupo Marco<p>Abstract</p> <p>Background</p> <p><it>Sinorhizobium meliloti </it>is a soil bacterium that forms nitrogen-fixing nodules on the roots of leguminous plants such as alfalfa (<it>Medicago sativa</it>). 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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>The obtained results allow to conclude that the symbiosis-required megaplasmid pSymA can be considered the major hot-spot for intra-specific differentiation in <it>S. meliloti</it>.</p>http://www.biomedcentral.com/1471-2164/6/158 |
| spellingShingle | Landry Christian R Aubin-Horth Nadia Cavalieri Duccio De Filippo Carlotta Mengoni Alessio Giuntini Elisa Becker Anke Bazzicalupo Marco Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of <it>Sinorhizobium meliloti </it>natural strains BMC Genomics |
| title | Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of <it>Sinorhizobium meliloti </it>natural strains |
| title_full | Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of <it>Sinorhizobium meliloti </it>natural strains |
| title_fullStr | Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of <it>Sinorhizobium meliloti </it>natural strains |
| title_full_unstemmed | Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of <it>Sinorhizobium meliloti </it>natural strains |
| title_short | Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of <it>Sinorhizobium meliloti </it>natural strains |
| title_sort | large scale genetic variation of the symbiosis required megaplasmid psyma revealed by comparative genomic analysis of it sinorhizobium meliloti it natural strains |
| url | http://www.biomedcentral.com/1471-2164/6/158 |
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