Universally distributed single-copy genes indicate a constant rate of horizontal transfer.
Universally distributed single-copy genes indicate a constant rate of horizontal transfer.
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DOI：
10.1371/journal.pone.0022099
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发表时间：
2011
期刊：
影响因子：
3.7
通讯作者：
Bork P
中科院分区：
文献类型：
--
作者：
Creevey CJ;Doerks T;Fitzpatrick DA;Raes J;Bork P
单拷贝基因普遍分布于生命的三个领域，编码翻译机制的大部分古老部分，被认为很少受到水平基因转移(HGT)的影响。事实上，有人提出它只发生在几个基因中，这意味着一种罕见的、可能并不有利的事件，在这种事件中，同源基因取代了原始基因，并且必须在外来环境中发挥作用(同源基因置换，OGD)。在这里，我们使用了一种基于保守的统计方法的自动识别HGT的方法，该方法能够稳健地分配捐赠者和接受者。应用于40个普遍存在的单拷贝基因，我们发现自上一个全球共同祖先(LUCA)以来，这些基因中出现了多达68个HGT(意味着OGD)，每个家族的比率为1.7。我们检查了一些被认为是HGT基础的因素，并在普遍分布的单拷贝基因子集中测试了它们的有效性。我们发现，不同的功能约束影响OGD的发生率，供体和受体在进化上越远，OGD发生的可能性就越小。此外，基因组较大的物种更有可能遭受OGD。最重要的是，无论上述趋势如何，OGD的数量都随着时间的推移呈线性增加，这表明OGD的速度是中性的、恒定的。这表明，高于这一比率的HGT水平可能表明，积极选择的转移可能允许利基适应或给予接受者有机体其他好处。
Single copy genes, universally distributed across the three domains of life and encoding mostly ancient parts of the translation machinery, are thought to be only rarely subjected to horizontal gene transfer (HGT). Indeed it has been proposed to have occurred in only a few genes and implies a rare, probably not advantageous event in which an ortholog displaces the original gene and has to function in a foreign context (orthologous gene displacement, OGD). Here, we have utilised an automatic method to identify HGT based on a conservative statistical approach capable of robustly assigning both donors and acceptors. Applied to 40 universally single copy genes we found that as many as 68 HGTs (implying OGDs) have occurred in these genes with a rate of 1.7 per family since the last universal common ancestor (LUCA). We examined a number of factors that have been claimed to be fundamental to HGT in general and tested their validity in the subset of universally distributed single copy genes. We found that differing functional constraints impact rates of OGD and the more evolutionarily distant the donor and acceptor, the less likely an OGD is to occur. Furthermore, species with larger genomes are more likely to be subjected to OGD. Most importantly, regardless of the trends above, the number of OGDs increases linearly with time, indicating a neutral, constant rate. This suggests that levels of HGT above this rate may be indicative of positively selected transfers that may allow niche adaptation or bestow other benefits to the recipient organism.
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