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揭示基因组序列熵和复杂度演化的模式。

Uncovering patterns of the evolution of genomic sequence entropy and complexity.

机构信息

Department of Bioprocess and Biotechnology, São Paulo State University (Unesp), Avenida Universitária, 3780, Botucatu, São Paulo, 18610-034, Brazil.

Department of Developmental Genetics, Max-Planck-Institut für Herz- Und Lungenforschung, Ludwigstr., 43, 61231, Bad Nauheim, Hessen, Germany.

出版信息

Mol Genet Genomics. 2021 Mar;296(2):289-298. doi: 10.1007/s00438-020-01729-y. Epub 2020 Oct 21.

Abstract

The lack of consensus concerning the biological meaning of entropy and complexity of genomes and the different ways to assess these data hamper conclusions concerning what are the causes of genomic entropy variation among species. This study aims to evaluate the entropy and complexity of genomic sequences of several species without using homologies to assess relationships among these variables and non-molecular data (e.g., the number of individuals) to seek a trigger of interspecific genomic entropy variation. The results indicate a relationship among genomic entropy, genome size, genomic complexity, and the number of individuals: species with a small number of individuals harbors large genome, and hence, low entropy but a higher complexity. We defined that the complexity of a genome relies on the entropy of each DNA segment within genome. Then, the entropy and complexity of a genome reflects its organization solely. Exons of vertebrates harbor smaller entropies than non-exon regions (likely by the repeats that accumulated from duplications), whereas other taxonomic groups do not present this pattern. Our findings suggest that small initial population might have defined current genomic entropy and complexity: actual genomes are less complex than ancestral ones. Besides, our data disagree with the relationship between phenotype and genomic entropies previously established. Finally, by establishing the relationship between genomic entropy/complexity with the number of individuals and genome size, under an evolutive perspective, ideas concerning the genomic variability may emerge.

摘要

由于缺乏对基因组熵和复杂性的生物学意义的共识,以及评估这些数据的不同方法,这阻碍了我们对导致物种间基因组熵变化的原因的结论。本研究旨在评估几个物种的基因组序列的熵和复杂性,而不使用同源性来评估这些变量之间的关系,也不使用非分子数据(例如个体数量)来寻找物种间基因组熵变化的触发因素。研究结果表明,基因组熵、基因组大小、基因组复杂性和个体数量之间存在关系:个体数量较少的物种拥有较大的基因组,因此,熵值较低,但复杂性较高。我们定义基因组的复杂性取决于基因组中每个 DNA 片段的熵。然后,基因组的熵和复杂性仅反映其组织。脊椎动物的外显子比非外显子区域具有更小的熵(可能是由于重复序列的积累),而其他分类群则没有这种模式。我们的研究结果表明,较小的初始种群可能决定了当前的基因组熵和复杂性:实际基因组比祖先基因组的复杂性要低。此外,我们的数据与之前建立的表型和基因组熵之间的关系不一致。最后,通过在进化视角下建立基因组熵/复杂性与个体数量和基因组大小之间的关系,可以出现有关基因组可变性的想法。

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