探索构建动物基因组序列进化关系中的客观特征集。

Exploring objective feature sets in constructing the evolution relationship of animal genome sequences.

机构信息

Laboratory of Theoretical Biophysics, School of Physical Science and Technology, Inner Mongolia University, Hohhot, 010021, China.

School of Economics and Management, Inner Mongolia University of Science and Technology, Baotou, 014010, China.

出版信息

BMC Genomics. 2023 Oct 24;24(1):634. doi: 10.1186/s12864-023-09747-x.

DOI:10.1186/s12864-023-09747-x

PMID:37872534

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10594854/

Abstract

BACKGROUND

Exploring evolution regularities of genome sequences and constructing more objective species evolution relationships at the genomic level are high-profile topics. Based on the evolution mechanism of genome sequences proposed in our previous research, we found that only the 8-mers containing CG or TA dinucleotides correlate directly with the evolution of genome sequences, and the relative frequency rather than the actual frequency of these 8-mers is more suitable to characterize the evolution of genome sequences.

RESULT

Therefore, two types of feature sets were obtained, they are the relative frequency sets of CG1 + CG2 8-mers and TA1 + TA2 8-mers. The evolution relationships of mammals and reptiles were constructed by the relative frequency set of CG1 + CG2 8-mers, and two types of evolution relationships of insects were constructed by the relative frequency sets of CG1 + CG2 8-mers and TA1 + TA2 8-mers respectively. Through comparison and analysis, we found that evolution relationships are consistent with the known conclusions. According to the evolution mechanism, we considered that the evolution relationship constructed by CG1 + CG2 8-mers reflects the evolution state of genome sequences in current time, and the evolution relationship constructed by TA1 + TA2 8-mers reflects the evolution state in the early stage.

CONCLUSION

Our study provides objective feature sets in constructing evolution relationships at the genomic level.

摘要

背景

探索基因组序列的演化规律，构建更客观的基因组水平物种进化关系是备受关注的课题。基于我们前期研究提出的基因组序列演化机制，我们发现只有包含 CG 或 TA 二核苷酸的 8 -mer 直接与基因组序列的演化相关，这些 8-mer 的相对频率而非实际频率更适合描述基因组序列的演化。

结果

因此，得到了两种特征集，即 CG1+CG2 8-mer 的相对频率集和 TA1+TA2 8-mer 的相对频率集。通过 CG1+CG2 8-mer 的相对频率集构建了哺乳动物和爬行动物的进化关系，通过 CG1+CG2 8-mer 和 TA1+TA2 8-mer 的相对频率集分别构建了昆虫的两种进化关系。通过比较和分析发现，进化关系与已知结论一致。根据演化机制，我们认为 CG1+CG2 8-mer 构建的进化关系反映了当前基因组序列的演化状态，而 TA1+TA2 8-mer 构建的进化关系反映了早期的演化状态。