Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains.
Large-scale genetic variation of the symbiosis-required megaplasmid pSymA revealed by comparative genomic analysis of Sinorhizobium meliloti natural strains.
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DOI：
10.1186/1471-2164-6-158
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发表时间：
2005-11-10
期刊：
影响因子：
4.4
通讯作者：
Bazzicalupo, Marco
中科院分区：
文献类型：
--
作者：
Giuntini, Elisa;Mengoni, Alessio;De Filippo, Carlotta;Cavalieri, Duccio;Aubin-Horth, Nadia;Landry, Christian R;Becker, Anke;Bazzicalupo, Marco
苜蓿中华根瘤菌是一种土壤细菌，可在苜蓿等豆科植物的根部形成固氮根瘤。该物种占据不同的生态位，作为自由生活的土壤细菌和植物根瘤的共生体存在。模式菌株 Rm 1021 的基因组包含一条染色体和两个大质粒，总基因组大小为 6 Mb。我们在寡核苷酸微阵列上应用了比较基因组杂交（CGH），以估计四种天然菌株在基因组水平上的遗传变异，其中两种是从意大利农业土壤中分离出来的，另两种是从咸海地区的沙漠土壤中分离出来的。与典型菌株 Rm 1021 相比，4.6% 至 5.7% 的基因显示出与缺失、核苷酸分歧或 ORF 重复一致的杂交模式。通过测序和 Southern 印迹证实了大量这些多态性。在 pSymA 巨质粒上发现了这些可变基因的统计显着部分，并分组为簇。发现这些可变基因主要是转座酶或功能未知的基因。所获得的结果可以得出这样的结论：共生所需的巨质粒pSymA可以被认为是苜蓿中华根瘤菌种内分化的主要热点。
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.