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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Whole-genome phylogeny of mammals: Evolutionary information in genie and nongenic regions
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Whole-genome phylogeny of mammals: Evolutionary information in genie and nongenic regions

机译：哺乳动物的全基因组系统发育：基因和非基因区域的进化信息

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摘要

Ten complete mammalian genome sequences were compared by using the "feature frequency profile" (FFP) method of alignment-free comparison. This comparison technique reveals that the whole nongenic portion of mammalian genomes contains evolutionary information that is similar to their genie counterparts-the intron and exon regions. We partitioned the complete genomes of mammals (such as human, chimp, horse, and mouse) into their constituent nongenic, intronic, and exonic components. Phylogenic species trees were constructed for each individual component class of genome sequence data as well as the whole genomes by using standard tree-building algorithms with FFP distances. The phylog-enies of the whole genomes and each of the component classes (exonic, intronic, and nongenic regions) have similar topologies, within the optimal feature length range, and all agree well with the evolutionary phylogeny based on a recent large dataset, multispecies, and multigene-based alignment. In the strictest sense, the FFP-based trees are genome phytogenies, not species phytogenies. However, the species phylogeny is highly related to the whole-genome phylogeny. Furthermore, our results reveal that the footprints of evolutionary history are spread throughout the entire length of the whole genome of an organism and are not limited to genes, introns, or short, highly conserved, nongenic sequences that can be adversely affected by factors (such as a choice of sequences, homoplasy, and different mutation rates) resulting in inconsistent species phytogenies.
机译：使用无比对比较的“特征频率曲线”（FFP）方法比较了十个完整的哺乳动物基因组序列。这种比较技术表明，哺乳动物基因组的整个非基因部分都包含与它们的基因对应部分（内含子和外显子区域）相似的进化信息。我们将哺乳动物（例如人，黑猩猩，马和小鼠）的完整基因组划分为其组成的非基因，内含子和外显子成分。通过使用具有FFP距离的标准树木构建算法，可以为基因组序列数据的每个单独组成类以及整个基因组构建系统发育树。在最佳特征长度范围内，整个基因组和每个组成部分类别（外显子，内含子和非基因区域）的系统同源性都具有相似的拓扑，并且都与基于最近的大型数据集，多物种的进化系统发育学非常吻合。 ，以及基于多基因的比对。从最严格的意义上说，基于FFP的树是基因组植物，而不是物种植物。但是，物种系统发育与全基因组系统发育高度相关。此外，我们的结果表明，进化史的足迹遍布生物体整个基因组的整个长度，并且不仅限于基因，内含子或可能受到多种因素不利影响的短的，高度保守的非基因序列（例如（序列选择，同质性和不同的突变率）导致物种植物遗传学不一致。

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