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| Status |
Public on May 01, 2009 |
| Title |
Genome Variation in the Symbiotic Nitrogen-Fixing Bacterium Sinorhizobium meliloti |
| Platform organism |
Sinorhizobium meliloti 1021 |
| Sample organism |
Sinorhizobium meliloti |
| Experiment type |
Genome variation profiling by array
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| Summary |
Differences in genome size and gene content are among the most important signatures of microbial adaptation and genome evolution. Here, we investigated the patterns of genome variation among strains of the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti. Using the sequenced strain Rm1021 as a reference, the genome size and gene content variations were analyzed among ten diverse natural strains, through pulse field gel electrophoresis (PFGE) and whole-genome microarray hybridizations. Our PFGE analysis showed a genome size range of 6.45-7.01Mbp, with the greatest variation arising from the pSymA replicon, followed by that of pSymB. No observable size difference was evident among the chromosomes. Consistent with this pattern of size differences, 41.2% of ORFs on pSymA were variably absent/present, followed by 12.7% on pSymB, and 3.7% on the chromosome. However, the percentages of ORFs that were variably duplicated were more evenly distributed among the three replicons, 11.0%, 16.5% and 15.3% respectively for ORFs on pSymA, pSymB and the chromosome. Among the 10 strains, the percentages of absent ORFs ranged from 1.51% to 6.35% and those of duplicated ORFs ranged from 0.27% to 8.56%. Our analyses showed that host plants, geographic origins, multilocus enzyme electrophoretic types, and replicon sizes had little influence on the distribution patterns of absent or duplicated ORFs. The proportions of ORFs that were either variably absent/present or variably duplicated differed greatly among the functional categories, for each of the three replicons as well as for the whole genome. Interestingly, we observed positive correlations among the three replicons in their numbers of absent ORFs as well as the numbers of duplicated ORFs, consistent with coordinated gene gains/losses in this important bacterium in nature.
microarray:Sm6kOligo
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| Overall design |
A total of 12 strains were included for the microarray analyses in this study. The 12 strains included two reference strains and ten other natural strains. Reference strain Rm1021 was the strain with a completely sequenced genome, from which the whole genome microarray was based on (Krol et al. 2004). The second reference strain RmF909 was derived from strain Rm1021 but with a deletion of 575 ORFs located on the megaplasmid pSymB (genomic location 106724-735431, Charles et al. 1991). The two reference strains were used for positive and negative controls in our microarray hybridization experiments and for establishing threshold values for determining whether an ORF is present or absent among natural strains.
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| Contributor(s) |
Guo H, Sun S, Eardly B, Finan T, Xu J |
| Citation(s) |
19935910 |
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| Submission date |
Apr 29, 2009 |
| Last update date |
Mar 21, 2012 |
| Contact name |
HONG GUO |
| Organization name |
MCMASTER UNIVERSITY
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| Department |
BIOLOGY
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| Lab |
DR.XU,JP
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| Street address |
1280Main St. West
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| City |
Hamilton |
| State/province |
Ontario |
| ZIP/Postal code |
L8S 4K1 |
| Country |
Canada |
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| Platforms (1) |
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| Samples (14)
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| Relations |
| BioProject |
PRJNA117055 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE15889_RAW.tar |
23.4 Mb |
(http)(custom) |
TAR (of GPR) |
| Processed data included within Sample table |
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