Genome phylogeny based on gene content
Genome phylogeny based on gene content
复制标题
DOI：
10.1038/5052
复制
发表时间：
1999-01-01
期刊：
影响因子：
30.8
通讯作者：
Huynen, MA
中科院分区：
文献类型：
--
作者：
Snel, B;Bork, P;Huynen, MA
由于水平基因转移（1），未被识别的旁系关系和高度可变的进化速率（2），从单个基因的比较中得出的物种遗传学很少相互一致。完全测序的基因组的出现允许构建对这种不一致性不太敏感并且比单基因树更能代表全基因组的同源性。在这里，我们提出了一个基于距离的植物发生（3）的基因内容的基础上，而不是序列的一致性，13个完全测序的基因组的单细胞物种。两个物种之间的相似性被定义为它们共有的基因数除以它们的基因总数。在这种类型的系统发育分析中，进化距离可以用进化事件（如基因的获得和丢失）来解释，而潜在的属性（基因内容）可以用功能来解释。因此，它处于基于单基因的遗传学和基于表型特征的遗传学的中间位置。尽管我们的综合基因组同源性独立于基于单个基因序列同一性水平的同源性，但它与基于16s rRNA序列相似性的原核同源性的标准参考相关（参考文献4）。因此，基因组之间共享的基因含量是由遗传学定量决定的，而不是由表型决定的，水平基因转移在决定基因组的基因含量方面只起有限的作用。
Species phylogenies derived from comparisons of single genes are rarely consistent with each other, due to horizontal gene transfer(1), unrecognized paralogy and highly variable rates of evolution(2). The advent of completely sequenced genomes allows the construction of a phylogeny that is less sensitive to such inconsistencies and more representative of whole-genomes than are single-gene trees. Here, we present a distance-based phytogeny(3) constructed on the basis of gene content, rather than on sequence identity, of 13 completely sequenced genomes of unicellular species. The similarity between two species is defined as the number of genes that they have in common divided by their total number of genes, Tn this type of phylogenetic analysis, evolutionary distance can be interpreted in terms of evolutionary events such as the acquisition and loss of genes, whereas the underlying properties (the gene content) can be interpreted in terms of function. As such, it takes a position intermediate to phylogenies based on single genes and phylogenies based on phenotypic characteristics. Although our comprehensive genome phylogeny is independent of phylogenies based on the level of sequence identity of individual genes, it correlates with the standard reference of prokarytic phylogeny based on sequence similarity of 16s rRNA (ref, 4). Thus, shared gene content between genomes is quantitatively determined by phylogeny, rather than by phenotype, and horizontal gene transfer has only a limited role in determining the gene content of genomes.