Kirzhner Valery, Bolshoy Alexander, Volkovich Zeev, Korol Abraham, Nevo Eviatar
Institute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel.
Biosystems. 2005 Sep;81(3):208-22. doi: 10.1016/j.biosystems.2005.04.003.
With the availability of genome sequences, the possibility of new phylogenetic reconstructions arises in order to reveal genomic relationships among organisms. According to the compositional-spectra (CS) approach proposed in our previous studies, any genomic sequence can be characterized by a distribution of frequencies of imperfect matching of words (oligonucleotides). In the current application of CS-analysis, we attempted to analyze the cluster structure of genomes across life. It appeared that compositional spectra show a clear three-group clustering of the compared prokaryotic and eukaryotic genomes. Unexpectedly, this grouping seriously differs from the classical Universal Tree of Life structure represented by common kingdoms known as Eubacteria, Archaebacteria, and Eukarya. The revealed CS-clustering displays high stability, putatively reflecting its objective nature, and still enigmatic biological significance that may result from convergent evolution driven by ecological selection. We believe that our approach provides a new and wider (compared to traditional methods) perspective of extracting genomic information of high evolutionary relevance.
随着基因组序列的可得性，出现了进行新的系统发育重建的可能性，以便揭示生物体之间的基因组关系。根据我们之前研究中提出的组成谱（CS）方法，任何基因组序列都可以通过单词（寡核苷酸）不完全匹配频率的分布来表征。在当前CS分析的应用中，我们试图分析整个生命过程中基因组的聚类结构。结果表明，组成谱显示出所比较的原核生物和真核生物基因组明显的三类聚类。出乎意料的是，这种分组与由真细菌、古细菌和真核生物等常见界所代表的经典通用生命树结构有很大不同。所揭示的CS聚类显示出高稳定性，推测反映了其客观性质，以及可能由生态选择驱动的趋同进化所导致的仍然神秘的生物学意义。我们相信，与传统方法相比，我们的方法为提取具有高度进化相关性的基因组信息提供了一个新的、更广泛的视角。
