微生物基因组通过短片段复制生长的证据
Evidence for growth of microbial genomes by short segmental duplications
摘要：
我们表明，微生物基因组的文本分析揭示了基因组早期进化的足迹。随机DNA序列在其四个核苷酸中被视为文本，其单词出现的频率预期服从泊松分布。值得注意的是，对于小于9个字母的单词，完整微生物基因组的分布的平均宽度是泊松分布的许多倍。我们对这一现象的解释如下：基因组是一个大系统，它具有一个小得多的“随机”系统的统计特性，我们现在看到的基因组的某些文本统计特性是它们祖先基因组的残余，它们比现在的基因组短得多。这种解释为基因组的增长提供了一个简单的生物学上合理的模型：基因组首先随机增长到大约1000个核苷酸（1k nt）的初始长度，或其最终长度的千分之一，然后主要通过随机片段复制增长。我们表明，使用平均约25 nt的重复片段，生成的模型序列具有当今基因组的统计特性。初始长度和复制片段长度都支持复制开始时的RNA世界。随机片段复制将极大地增强基因组重复使用其难以获得的代码的能力，并且实践它的基因组将比那些没有的进化得快得多。
英文摘要：
We show that textual analysis of microbial genomes reveal telling footprints of the early evolution of the genomes. The frequencies of word occurrence of random DNA sequences considered as texts in their four nucleotides are expected to obey Poisson distributions. It is noticed that for words less than nine letters the average width of the distributions for complete microbial genomes is many times that of a Poisson distribution. We interpret this phenomenon as follows: the genome is a large system that possesses the statistical characteristics of a much smaller ``random'' system, and certain textual statistical properties of genomes we now see are remnants of those of their ancestral genomes, which were much shorter than the genomes are now. This interpretation suggests a simple biologically plausible model for the growth of genomes: the genome first grows randomly to an initial length of approximately one thousand nucleotides (1k nt), or about one thousandth of its final length, thereafter mainly grows by random segmental duplication. We show that using duplicated segments averaging around 25 nt, the model sequences generated possess statistical properties characteristic of present day genomes. Both the initial length and the duplicated segment length support an RNA world at the time duplication began. Random segmental duplication would greatly enhance the ability of a genome to use its hard-to-acquire codes repeatedly, and a genome that practiced it would have evolved enormously faster than those that did not.
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