Center for Environmental Genomics, Department of Biology, McMaster University, Hamilton, ON L8S 4K1, Canada.
Genome. 2009 Oct;52(10):862-75. doi: 10.1139/g09-060.
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 10 natural strains of the symbiotic nitrogen-fixing bacterium Sinorhizobium meliloti, using pulse field gel electrophoresis (PFGE) and whole-genome microarray hybridizations. Our PFGE analysis showed a genome size range of 6.45-7.01 Mbp, with the greatest variation arising from the pSymA replicon, followed by pSymB; no size difference was evident among the chromosomes. Consistent with this pattern of size differences, 41.2% of open reading frames (ORFs) on pSymA were variably absent/present, followed by 12.7% on pSymB and 3.7% on the chromosome. However, the ORFs that were variably duplicated were more evenly distributed among the three replicons: 11.0%, 16.5%, and 15.3% of ORFs on pSymA, pSymB, and the chromosome, respectively. Among the 10 strains, the percentage of ORFs that were absent ranged from 1.51% to 6.35%, and the percentage of ORFs that were duplicated 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 the number of absent ORFs as well as the number of duplicated ORFs, consistent with coordinated gene gains and losses in this important bacterium in nature.
基因组大小和基因组成分的差异是微生物适应和基因组进化的最重要特征之一。在这里，我们使用脉冲场凝胶电泳 (PFGE) 和全基因组微阵列杂交技术，研究了共生固氮菌根瘤菌 10 个天然菌株的基因组变异模式。我们的 PFGE 分析显示，基因组大小范围为 6.45-7.01 Mbp，最大的变异来自 pSymA 复制子，其次是 pSymB；染色体之间没有明显的大小差异。与这种大小差异模式一致，pSymA 上的 41.2%的开放阅读框 (ORF) 可出现不同程度的缺失/存在，其次是 pSymB 上的 12.7%和染色体上的 3.7%。然而，可发生可变复制的 ORF 则更均匀地分布在三个复制子中：pSymA、pSymB 和染色体上的 ORF 分别有 11.0%、16.5%和 15.3%是可变复制的。在这 10 个菌株中，缺失的 ORF 百分比范围为 1.51%至 6.35%，复制的 ORF 百分比范围为 0.27%至 8.56%。我们的分析表明，宿主植物、地理位置、多基因酶电泳类型和复制子大小对缺失或复制的 ORF 分布模式几乎没有影响。每个复制子以及整个基因组的功能类别中，可发生可变缺失/存在或可变复制的 ORF 比例差异很大。有趣的是，我们观察到三个复制子之间缺失的 ORF 数量和复制的 ORF 数量之间存在正相关，这与该重要细菌在自然界中的协同基因增益和缺失一致。
