The human phylome.
The human phylome.
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人类的前线。
DOI：
10.1186/gb-2007-8-6-r109
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发表时间：
2007
期刊：
影响因子：
12.3
通讯作者：
中科院分区：
文献类型：
--
作者：
重建了人类系统发育树，其中包括39种全序列真核生物中所有人类蛋白质及其同源物的进化关系。系统基因组学分析有助于建立生物体及其基因之间的进化关系。一个植物系统，即一个基因组中所有基因同源性的完整集合，构成了一个有价值的信息来源，但它在大型基因组中的应用仍然构成了一个技术挑战。使用系统发育树还需要发展新的方法来帮助我们解释它们。我们在这里重建人类的系统发育，其中包括所有人类蛋白质和它们的同源物之间的39个完全测序的真核生物的进化关系。系统发生学的技术包括对齐修剪，分支长度优化，进化模型测试和最大似然和贝叶斯方法。虽然与其他拓扑结构的差异很小，但大多数树木支持腔肠动物和Unikont假说，以及排除啮齿动物的灵长类动物与laurasatheria的分组。我们评估基因重复事件的程度及其与所涉及的蛋白质家族的功能作用的关系。我们发现支持至少一个，可能是两个，脊椎动物辐射前的全基因组复制轮。使用一种新的算法，这是独立于一个物种的同源性，我们得到的直系和旁系关系的人类蛋白质真核生物基因组。预计不同基因的系统发育之间会出现拓扑变异，这凸显了系统基因组分析中基因采样效应的危险。在某些系统发生分裂时复制的基因家族的功能与这些谱系中的主要进化转变之间可以建立几种联系。这里实现的管道可以很容易地适应其他生物体的使用。
The human phylome, which includes evolutionary relationships of all human proteins and their homologs among thirty-nine fully sequenced eukaryotes, is reconstructed. Phylogenomics analyses serve to establish evolutionary relationships among organisms and their genes. A phylome, the complete collection of all gene phylogenies in a genome, constitutes a valuable source of information, but its use in large genomes still constitutes a technical challenge. The use of phylomes also requires the development of new methods that help us to interpret them. We reconstruct here the human phylome, which includes the evolutionary relationships of all human proteins and their homologs among 39 fully sequenced eukaryotes. Phylogenetic techniques used include alignment trimming, branch length optimization, evolutionary model testing and maximum likelihood and Bayesian methods. Although differences with alternative topologies are minor, most of the trees support the Coelomata and Unikont hypotheses as well as the grouping of primates with laurasatheria to the exclusion of rodents. We assess the extent of gene duplication events and their relationship with the functional roles of the protein families involved. We find support for at least one, and probably two, rounds of whole genome duplications before vertebrate radiation. Using a novel algorithm that is independent from a species phylogeny, we derive orthology and paralogy relationships of human proteins among eukaryotic genomes. Topological variations among phylogenies for different genes are to be expected, highlighting the danger of gene-sampling effects in phylogenomic analyses. Several links can be established between the functions of gene families duplicated at certain phylogenetic splits and major evolutionary transitions in those lineages. The pipeline implemented here can be easily adapted for use in other organisms.