Compositional differences within and between eukaryotic genomes
Compositional differences within and between eukaryotic genomes
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DOI：
10.1073/pnas.94.19.10227
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发表时间：
1997-09-16
影响因子：
11.1
通讯作者：
Mrazek, J
中科院分区：
文献类型：
--
作者：
Karlin, S;Mrazek, J
真核生物基因组的相似性关系是利用来自大量基因组序列的序列信息推断出来的。物种样本序列内部和之间的比较基于二核苷酸相对丰度值的谱图(所有XY的谱图为rho(XY)* = f(XY)*/f(X)*f(Y)*，其中f（X)*表示核苷酸X的频率，f(XY)*表示二核苷酸XY的频率，两者都是从与其反向补体连接的序列中计算出来的）。以往关于原核生物的研究和本研究表明，同一生物不同DNA序列样本（样本量大于或等于50 kb）的谱图彼此之间的相似性通常远高于其他生物的谱图，亲缘关系近的生物通常比远缘关系近的生物具有更多的相似谱图，在此基础上，我们将集合{rho(XY)*}作为基因组标记。本文鉴定了rho(XY)*极端，并比较了多种真核生物物种的基因组特征差异。对维持这些特征差异的机制的解释主要集中在全基因组复制、修复、DNA结构和上下文相关的突变偏差上。研究还发现，物种之间线粒体基因组特征的差异与相应的核基因组特征差异相似，尽管相应的线粒体和核特征之间存在很大差异。基因组特征的差异也暗示了啮齿动物和其他哺乳动物之间的差异，以及单子叶植物和双子叶植物之间的差异，并为真菌和原生生物的多样性之间的相似性提供了证据。
Eukaryotic genome similarity relationships are inferred using sequence information derived from large aggregates of genomic sequences. Comparisons within and between species sample sequences are based on the profile of dinucleotide relative abundance values (The profile is rho(XY)* = f(XY)*/f(X)*f(Y)* for all XY, where f(X)* denotes the frequency of the nucleotide X and f(XY)* denotes the frequency of the dinucleotide XY, both computed from the sequence concatenated with its inverted complement), Previous studies with respect to prokaryotes and this study document that profiles of different DNA sequence samples (sample size greater than or equal to 50 kb) from the same organism are generally much more similar to each other than they are to profiles from other organisms, and that closely related organisms generally have more similar profiles than do distantly related organisms, On this basis we refer to the collection {rho(XY)*} as the genome signature. This paper identifies rho(XY)* extremes and compares genome signature differences for a diverse range of eukaryotic species. Interpretations on the mechanisms maintaining these profile differences center on genome-wide replication, repair, DNA structures, and context-dependent mutational biases, It is also observed that mitochondrial genome signature differences between species parallel the corresponding nuclear genome signature differences despite large differences between corresponding mitochondrial and nuclear signatures. The genome signature differences also have implications for contrasts between rodents and other mammals, and between monocot and dicot plants, as well as providing evidence for similarities among fungi and the diversity of protists.