Laboratory of Theoretical Biophysics, School of Physical Science & Technology, Inner Mongolia University, Hohhot, 010021, China.
School of Economics and Management, Inner Mongolia University of Science & Technology, Baotou, 014010, China.
BMC Evol Biol. 2020 Nov 23;20(1):157. doi: 10.1186/s12862-020-01723-3.
K-mer spectra of DNA sequences contain important information about sequence composition and sequence evolution. We want to reveal the evolution rules of genome sequences by studying the k-mer spectra of genome sequences.
The intrinsic laws of k-mer spectra of 920 genome sequences from primate to prokaryote were analyzed. We found that there are two types of evolution selection modes in genome sequences, named as CG Independent Selection and TA Independent Selection. There is a mutual inhibition relationship between CG and TA independent selections. We found that the intensity of CG and TA independent selections correlates closely with genome evolution and G + C content of genome sequences. The living habits of species are related closely to the independent selection modes adopted by species genomes. Consequently, we proposed an evolution mechanism of genomes in which the genome evolution is determined by the intensities of the CG and TA independent selections and the mutual inhibition relationship. Besides, by the evolution mechanism of genomes, we speculated the evolution modes of prokaryotes in mild and extreme environments in the anaerobic age and the evolving process of prokaryotes from anaerobic to aerobic environment on earth as well as the originations of different eukaryotes.
We found that there are two independent selection modes in genome sequences. The evolution of genome sequence is determined by the two independent selection modes and the mutual inhibition relationship between them.
DNA 序列的 K-mer 频谱包含有关序列组成和序列进化的重要信息。我们希望通过研究基因组序列的 K-mer 频谱来揭示基因组序列的进化规律。
分析了来自灵长类动物到原核生物的 920 个基因组序列的 K-mer 频谱的内在规律。我们发现基因组序列中存在两种进化选择模式，分别称为 CG 独立选择和 TA 独立选择。CG 和 TA 独立选择之间存在相互抑制关系。我们发现 CG 和 TA 独立选择的强度与基因组进化和基因组序列的 G+C 含量密切相关。物种的生活习性与物种基因组采用的独立选择模式密切相关。因此，我们提出了一种基因组进化机制，其中基因组进化由 CG 和 TA 独立选择的强度和相互抑制关系决定。此外，通过基因组的进化机制，我们推测了在厌氧时代，原核生物在温和和极端环境中的进化模式，以及原核生物从厌氧到有氧环境的进化过程，以及不同真核生物的起源。
我们发现基因组序列中存在两种独立的选择模式。基因组序列的进化由这两种独立的选择模式及其相互抑制关系决定。
