基于共同前缀位置的哺乳动物mtDNA序列系统发育分析
Phylogenetic Analysis of Mammalian mtDNA Sequences Based on Common Prefix Positions
DOI: 10.12677/OJNS.2021.92030, PDF,  被引量   
作者: 陆 超, 王 代：辽宁师范大学，辽宁 大连
关键词: 哺乳动物；DNA序列；前缀集；系统发育分析；Mammal； DNA Sequence； PrefixSet； Phylogenetic Analysis
摘要: 本文基于共同前缀标识符，通过环形前缀树法构建DNA序列的环形前缀树，得到能够表征序列信息的前缀集，去除生物序列长度对序列间距离计算的影响的同时并考虑序列对的共同前缀位置等因素，创建了一种新的非比对方法——基于共同前缀的位置差法，选取含有80条哺乳动物的mtDNA序列的数据集作为测试对象，运用邻接(Neighbor-Joining)法构建系统发育树，快速且准确地得到符合生物学分类的结果。
Abstract: This paper is based on the common prefix identifier. A circular prefix tree of DNA sequences is constructed by the circular prefix tree method to obtain a prefix set that can characterize sequence information, which removed the influence of biological sequence length on the calculation of the distance between sequences, and considered the common prefix position of sequence pairs. And other factors, created a new non-comparison method—the position difference method based on the common prefix. The data set containing 80 mammalian mtDNA sequences was selected as the test object, and the phylogenetic tree was constructed using the Neighbor-Joining method, which could fast and accurately get the results that meet the biological classification.
文章引用：陆超, 王代. 基于共同前缀位置的哺乳动物mtDNA序列系统发育分析[J]. 自然科学, 2021, 9(2): 272-280. https://doi.org/10.12677/OJNS.2021.92030

参考文献

[1] Saw, A.K., Raj, G., Das, M., et al. (2019) Alignment-Free Method for DNA Sequence Clustering Using Fuzzy Integral Similarity. Scientific Reports, 9, Article No. 3753. [Google Scholar] [CrossRef] [PubMed]
[2] Vinga, S. and Almeida, J. (2003) Alignment-Free Sequence Comparison—A Review. Bioinforma, 19, 513-523. [Google Scholar] [CrossRef] [PubMed]
[3] Zielezinski, A., Vinga, S., Almeida, J. and Karlowski, W.M. (2017) Align-ment-Free Sequence Comparison: Benefits, Applications, and Tools. Genome Biology, 18, Article No. 186. [Google Scholar] [CrossRef] [PubMed]
[4] Bernard, G., Chan, C.X., Chan, Y.-B., et al. (2017) Alignment-Free Inference of Hierarchical and Reticulate Phylogenomic Relationships. Briefings in Bioinformatics, 20, 426-435.
[5] Zhao, B., He, R.L. and Yau, S.S.-T. (2011) A New Distribution Vector and Its Application in Genome Clustering. Molecular Phylogenetics and Evolution, 59, 438-443. [Google Scholar] [CrossRef] [PubMed]
[6] Weiner, P. (1973) Linear Pattern Matching Algorithms. Proceedings of the 14th Annual IEEE Symposium on Switching and Automata Theory, USA, 15-17 October 1973, 1-11. [Google Scholar] [CrossRef] 
[7] 张欣. 基于后缀树的DNA序列进化树构建研究[D]: [硕士学位论文]. 大连: 辽宁师范学, 2019。
[8] Anderson, S., De Bruijn, M.H.L., Coulson, A.R., et al. (1982) Complete Sequence of Bovine Mitochondrial DNA Conserved Features of the Mammalian Mitochondrial Genome. Journal of Molecular Biology, 156, 683-717. [Google Scholar] [CrossRef] 
[9] Saitou, N. and Nei, M. (1987) The Neighbor-Joining Method: A New Method for Reconstructing Phylogenetic Trees. Molecular Biology and Evolution, 4, 406-425.
[10] Murphy, W.J., Eizirik, E., Johnson, W.E., et al. (2001) Molecular Phylogenetics and the Origins of Placental Mammals. Nature, 409, 614-618. [Google Scholar] [CrossRef] [PubMed]
[11] Kjer, K.M. and Honeycutt, R.L. (2007) Site Specific Rates of Mitochondrial Genomes and the Phylogeny of Eutheria. BioMed Central Evolutionary Biology, 7, Article No. 8. [Google Scholar] [CrossRef] [PubMed]
[12] Xie, X.H., Yu, Z.G., Han, G.S., Yang, W.F. and Anh, V. (2015) Whole-Proteome Based Phylogenetic Tree Construction with Inter-Amino-Acid Distances and the Conditional Geometric Distribution Profiles. Molecu-lar Phylogenetics and Evolution, 89, 37-45. [Google Scholar] [CrossRef] [PubMed]
[13] Agnarsson, I., Kuntner, M. and May-Collado, L.J. (2010) Dogs, Cats, and Kin: A Molecular Species-Level Phylogeny of Carnivora. Molecular Phylogenetics and Evolution, 54, 726-745. [Google Scholar] [CrossRef] [PubMed]
[14] Zurano, J.P., Magalhães, F.M., Asato, A.E., et al. (2019) Cetartiodactyla: Updating a Time-Calibrated Molecular Phylogeny. Molecular Phylogenetics and Evolution, 133, 256-262. [Google Scholar] [CrossRef] [PubMed]
[15] Dos Reis, M., Gunnell, G.F., Barba-Montoya, J., et al. (2018) Using Phylo-genomic Data to Explore the Effects of Relaxed Clocks and Calibration Strategies on Divergence Time Estimation: Primates as a Test Case. Systematic Biology, 67, 594-615. [Google Scholar] [CrossRef] [PubMed]
[16] Steppan, S.J. and Schenk, J.J. (2017) Muroid Rodent Phylogenetics: 900-Species Tree Reveals Increasing Diversification Rates. PLoS ONE, 12, e0183070. [Google Scholar] [CrossRef] [PubMed]