Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution
Ancestral genome sizes specify the minimum rate of lateral gene transfer during prokaryote evolution
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DOI：
10.1073/pnas.0606318104
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发表时间：
2007-01-16
影响因子：
11.1
通讯作者：
Martin, William
中科院分区：
文献类型：
--
作者：
Dagan, Tal;Martin, William
在微生物进化中发生的横向基因转移（LGT）的数量存在很大争议。通过基因树比较量化LGT的努力估计，所有原核基因中有2%至60%受到LIST的影响，30倍的差异反映了研究的基因样本之间的差异和系统发育重建中固有的不确定性。在这里，我们提出了一个简单的方法，是独立的基因树比较，估计测序的原核基因组之间的LGT率。如果在进化过程中很少或根本没有发生LIST，祖先的基因组大小将变得不切实际地大，而太多的LGT将使它们变得太小。我们确定了LGT的量，这是必要的，足以使推断的祖先基因组大小的分布与现代微生物中观察到的一致。我们假设所有基因树都是兼容的，而不是测试基因间的系统发育一致性或缺乏一致性;因此，我们的方法提供了非常保守的平均LGT率的下限估计。结果表明，在分布在190个测序基因组中的57，670个基因家族中，至少有三分之二，甚至可能是全部，在其进化史上的某个时期受到了LIST的影响。然而，在基因分布模式中仍然可以检测到共同祖先的成分。我们估计所有基因的平均LGT率的最小下限为每个基因家族和基因家族寿命1.1个LGT事件，并且当仅存在于少数基因组中的基因被排除在分析之外时，该最小率急剧增加。
The amount of lateral gene transfer (LGT) that has occurred in microbial evolution is heavily debated. Efforts to quantify LGT through gene-tree comparisons have delivered estimates that between 2% and 60% of all prokaryotic genes have been affected by LIST, the 30-fold discrepancy reflecting differences among gene samples studied and uncertainties inherent in phylogenetic reconstruction. Here we present a simple method that is independent of gene-tree comparisons to estimate the LGT rate among sequenced prokaryotic genomes. If little or no LIST has occurred during evolution, ancestral genome sizes would become unrealistically large, whereas too much LGT would render them far too small. We determine the amount of LGT that is necessary and sufficient to bring the distribution of inferred ancestral genome sizes into agreement with that observed among modern microbes. Rather than testing for phylogenetic congruence or lack thereof across genes, we assume that all gene trees are compatible; hence, our method delivers very conservative lower-bound estimates of the average LGT rate. The results indicate that among 57,670 gene families distributed across 190 sequenced genomes, at least two-thirds and probably all, have been affected by LIST at some time in their evolutionary past. A component of common ancestry nonetheless remains detectable in gene distribution patterns. We estimate the minimum lower bound for the average LGT rate across all genes as 1.1 LGT events per gene family and gene family lifespan and this minimum rate increases sharply when genes present in only a few genomes are excluded from the analysis.