Reconstructing Phylogenetic Trees of Prokaryote Genomes by Randomly Sampling Oligopeptides
Reconstructing Phylogenetic Trees of Prokaryote Genomes by Randomly Sampling Oligopeptides
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DOI：
10.1007/11428848_116
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发表时间：
2005-05
影响因子：
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通讯作者：
O. Maruyama;A. Matsuda;S. Kuhara
中科院分区：
文献类型：
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作者：
O. Maruyama;A. Matsuda;S. Kuhara
在本文中，我们提出了一种从原核生物的完整蛋白质组中随机抽取相对较小的固定长度的寡肽来重建系统发育树的方法。对于每个生物体，采样的寡肽的频率向量被生成，并被用作重建系统发生树的构建块。通过这个过程，独立地创建多个系统发育树，并创建这些树的共识树。我们已经将我们的方法应用于一组109种生物，包括16种古生菌、87种细菌和6种真核生物，在重建单个系统发育树时，使用了长度为5的所有3,200,000个寡肽中的约10%。我们的共识树与Bergey‘s手册中的树在大多数基本分类群上是一致的。此外，它们与用齐等人给出的长度为K=5和6的所有20K寡肽重建的相同生物体的树具有几乎相同的质量。因此，我们可以得出结论，相对较少的长度为5的寡肽的频率，即使这些寡肽是以随机方法确定的，也具有几乎与所有长度为5或6的寡肽的频率相同的系统发育信息。
In this paper, we propose a method for reconstructing phylogenetic trees of a given set of prokaryote organisms by randomly sampling relatively small oligopeptides of a fixed length from their complete proteomes. For each of the organisms, a vector of frequencies of the sampled oligopeptides is generated and used as a building block in reconstructing phylogenetic trees. By this procedure, multiple phylogenetic trees are created independently, and a consensus tree of those trees is created. We have applied our method to a set of 109 organisms, including 16 Archaea, 87 Bacteria, and 6 Eukarya, using around 10% of all the 3,200,000 oligopeptides of length 5 in a reconstruction of a single phylogenetic tree. Our consensus tree agrees with the tree of Bergey's Manual in most of the basic taxa. In addition, they have almost the same quality as the trees of the same organisms reconstructed using all the 20Koligopeptides of length K = 5 and 6 given by Qi et al. Thus we can conclude that, the frequencies of a relatively small number of oligopeptides of length 5, even if those oligopeptides are determined in a random method, has phylogenetic information almost equivalent to the frequencies of all the oligopeptides of length 5 or 6.