Grogan Dennis W, Ozarzak Melissa A, Bernander Rolf
Department of Biological Sciences, University of Cincinnati, Cincinnati, OH 45221-0006, USA.
Environ Microbiol. 2008 Jan;10(1):137-46. doi: 10.1111/j.1462-2920.2007.01439.x. Epub 2007 Sep 11.
The ability of competitive (i.e., comparative) genomic hybridization (CGH) to assess similarity across entire microbial genomes suggests that it should reveal diversification within and between natural populations of free-living prokaryotes. We used CGH to measure relatedness of genomes drawn from Sulfolobus populations that had been shown in a previous study to be diversified along geographical lines. Eight isolates representing a wide range of spatial separation were compared with respect to gene-specific tags based on a closely related reference strain (Sulfolobus solfataricus P2). For the purpose of assessing genetic divergence, 232 loci identified as polymorphic were assigned one of two alleles based on the corresponding fluorescence intensities from the arrays. Clustering of these binary genotypes was stable with respect to changes in the threshold and similarity criteria, and most of the groupings were consistent with an isolation-by-distance model of diversification. These results indicate that increasing spatial separation of geothermal sites correlates not only with minor sequence polymorphisms in conserved genes of Sulfolobus (demonstrated in the previous study), but also with the regions of difference (RDs) that occur between genomes of conspecifics. In view of the abundance of RDs in prokaryotic genomes and the relevance that some RDs may have for ecological adaptation, the results further suggest that CGH on microarrays may have advantages for investigating patterns of diversification in other free-living archaea and bacteria.
竞争性（即比较性）基因组杂交（CGH）评估整个微生物基因组相似性的能力表明，它应该能够揭示自由生活原核生物自然种群内部和之间的多样性。我们使用CGH来测量从硫磺菌种群中提取的基因组的相关性，在之前的一项研究中已表明这些种群沿地理线存在多样性。基于密切相关的参考菌株（嗜热栖热菌P2），对代表广泛空间分离范围的八个分离株进行了基因特异性标签方面的比较。为了评估遗传差异，根据阵列中相应的荧光强度，将鉴定为多态性的232个基因座分配为两个等位基因之一。这些二元基因型的聚类在阈值和相似性标准变化方面是稳定的，并且大多数分组与距离隔离的多样化模型一致。这些结果表明，地热位点空间分离的增加不仅与硫磺菌保守基因中的微小序列多态性相关（在之前的研究中已证明），而且与同种基因组之间出现的差异区域（RDs）相关。鉴于原核生物基因组中RDs的丰富性以及一些RDs可能与生态适应相关，这些结果进一步表明，微阵列上的CGH在研究其他自由生活古菌和细菌的多样化模式方面可能具有优势。
