Genome dynamics in a natural archaeal population
Genome dynamics in a natural archaeal population
复制标题
DOI：
10.1073/pnas.0604851104
复制
发表时间：
2007-02-06
影响因子：
11.1
通讯作者：
Banfield, Jillian F.
中科院分区：
文献类型：
--
作者：
Allen, Eric E.;Tyson, Gene W.;Banfield, Jillian F.
从基因组异质性的形式和分布可以推断出引起和限制菌株种群内多样化的进化过程。区分嗜酸性古菌Ferroplasma acidarmanus fer1从同一地点，fer1（env）的同一物种的环境人口的基因组变化的程度，确定通过比较1.94兆碱基（Mb）的基因组序列的分离与重建从8 Mb的环境序列数据。fer 1（env）复合序列采样了约92%的分离株基因组。环境序列数据也进行了分析，以揭示共存，共同进化的fer1（env）人口的基因组异质性。分析表明，转座酶的运动和插入和可能的噬菌体起源的新基因块的丢失发生迅速足以引起在当地人口的基因内容的异质性。由于环境DNA来自许多密切相关的个体，因此可以量化种群内的基因序列变异性。除了少数基因变异外，所有的基因变异都显示出强烈的净化选择的证据。基于少数不同的序列类型和它们的分布，我们推断该种群正在经历频繁的遗传重组，从而形成了一个由选择塑造的镶嵌基因组库。相对于种群中的个体而言，种群具有更大的遗传潜力，而且组合过程产生了许多密切相关的基因组类型，这可能为适应环境波动提供了基础。
Evolutionary processes that give rise to, and limit, diversification within strain populations can be deduced from the form and distribution of genomic heterogeneity. The extent of genomic change that distinguishes the acidophilic archaeon Ferroplasma acidarmanus fer1 from an environmental population of the same species from the same site, fer1 (env), was determined by comparing the 1.94-megabase (Mb) genome sequence of the isolate with that reconstructed from 8 Mb of environmental sequence data. The fer1(env) composite sequence sampled approximate to 92% of the isolate genome. Environmental sequence data were also analyzed to reveal genomic heterogeneity within the coexisting, coevolving fer1(env) population. Analyses revealed that transposase movement and the insertion and loss of blocks of novel genes of probable phage origin occur rapidly enough to give rise to heterogeneity in gene content within the local population. Because the environmental DNA was derived from many closely related individuals, it was possible to quantify gene sequence variability within the population. All but a few gene variants show evidence of strong purifying selection. Based on the small number of distinct sequence types and their distribution, we infer that the population is undergoing frequent genetic recombination, resulting in a mosaic genome pool that is shaped by selection. The larger genetic potential of the population relative to individuals within it and the combinatorial process that results in many closely related genome types may provide the basis for adaptation to environmental fluctuations.