Intrinsic Laws of K-mer Spectra of Genome Sequences and Evolution Mechanism of Genomes

Overview

Journal BMC Evol Biol

Publisher Biomed Central

Specialty Biology

Date 2020 Nov 24

PMID 33228538

Citations 5

Authors

Zhenhua Yang

Hong Li

Yun Jia

Yan Zheng

Hu Meng

Tonglaga Bao

Xiaolong Li

Liaofu Luo

Affiliations

Soon will be listed here.

Abstract

Background: 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.

Results: 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.

Conclusion: 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.

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References

Down T, Hubbard T . Computational detection and location of transcription start sites in mammalian genomic DNA. Genome Res. 2002; 12(3):458-61. PMC: 155284. DOI: 10.1101/gr.216102. View

Kwok A, Su S, Reynolds R, Bay S, Av-Gay Y, Dovichi N . Species identification and phylogenetic relationships based on partial HSP60 gene sequences within the genus Staphylococcus. Int J Syst Bacteriol. 1999; 49 Pt 3:1181-92. DOI: 10.1099/00207713-49-3-1181. View

Hirt R, Logsdon Jr J, Healy B, Dorey M, Doolittle W, Embley T . Microsporidia are related to Fungi: evidence from the largest subunit of RNA polymerase II and other proteins. Proc Natl Acad Sci U S A. 1999; 96(2):580-5. PMC: 15179. DOI: 10.1073/pnas.96.2.580. View

Karlin S, Mrazek J . Compositional differences within and between eukaryotic genomes. Proc Natl Acad Sci U S A. 1997; 94(19):10227-32. PMC: 23344. DOI: 10.1073/pnas.94.19.10227. View

Chen Y, Nyeo S, Yeh C . Model for the distributions of k-mers in DNA sequences. Phys Rev E Stat Nonlin Soft Matter Phys. 2005; 72(1 Pt 1):011908. DOI: 10.1103/PhysRevE.72.011908. View

Qi J, Luo H, Hao B . CVTree: a phylogenetic tree reconstruction tool based on whole genomes. Nucleic Acids Res. 2004; 32(Web Server issue):W45-7. PMC: 441500. DOI: 10.1093/nar/gkh362. View

Ulitsky I, Burstein D, Tuller T, Chor B . The average common substring approach to phylogenomic reconstruction. J Comput Biol. 2006; 13(2):336-50. DOI: 10.1089/cmb.2006.13.336. View

Zhang Q, Jun S, Leuze M, Ussery D, Nookaew I . Viral Phylogenomics Using an Alignment-Free Method: A Three-Step Approach to Determine Optimal Length of k-mer. Sci Rep. 2017; 7:40712. PMC: 5244389. DOI: 10.1038/srep40712. View

Ciccarelli F, Doerks T, von Mering C, Creevey C, Snel B, Bork P . Toward automatic reconstruction of a highly resolved tree of life. Science. 2006; 311(5765):1283-7. DOI: 10.1126/science.1123061. View

10.

Raime K, Remm M . Method for the Identification of Taxon-Specific -mers from Chloroplast Genome: A Case Study on Tomato Plant (). Front Plant Sci. 2018; 9:6. PMC: 5776150. DOI: 10.3389/fpls.2018.00006. View

11.

Zheng Y, Li H, Wang Y, Meng H, Zhang Q, Zhao X . Evolutionary mechanism and biological functions of 8-mers containing CG dinucleotide in yeast. Chromosome Res. 2017; 25(2):173-189. DOI: 10.1007/s10577-017-9554-z. View

12.

Hysom D, Naraghi-Arani P, Elsheikh M, Carrillo A, Williams P, Gardner S . Skip the alignment: degenerate, multiplex primer and probe design using K-mer matching instead of alignments. PLoS One. 2012; 7(4):e34560. PMC: 3317645. DOI: 10.1371/journal.pone.0034560. View

13.

Chen W, Feng P, Deng E, Lin H, Chou K . iTIS-PseTNC: a sequence-based predictor for identifying translation initiation site in human genes using pseudo trinucleotide composition. Anal Biochem. 2014; 462:76-83. DOI: 10.1016/j.ab.2014.06.022. View

14.

Carvalho A, Dupim E, Goldstein G . Improved assembly of noisy long reads by k-mer validation. Genome Res. 2016; 26(12):1710-1720. PMC: 5131822. DOI: 10.1101/gr.209247.116. View

15.

Izan S, Esselink D, Visser R, Smulders M, Borm T . Assembly of Complete Chloroplast Genomes from Non-model Species Based on a K-mer Frequency-Based Selection of Chloroplast Reads from Total DNA Sequences. Front Plant Sci. 2017; 8:1271. PMC: 5539191. DOI: 10.3389/fpls.2017.01271. View

16.

Pace N, Sapp J, Goldenfeld N . Phylogeny and beyond: Scientific, historical, and conceptual significance of the first tree of life. Proc Natl Acad Sci U S A. 2012; 109(4):1011-8. PMC: 3268332. DOI: 10.1073/pnas.1109716109. View

17.

Ludwig W, Strunk O, Klugbauer S, Klugbauer N, Weizenegger M, Neumaier J . Bacterial phylogeny based on comparative sequence analysis. Electrophoresis. 1998; 19(4):554-68. DOI: 10.1002/elps.1150190416. View

18.

Wen J, Chan R, Yau S, He R, Yau S . K-mer natural vector and its application to the phylogenetic analysis of genetic sequences. Gene. 2014; 546(1):25-34. PMC: 4096558. DOI: 10.1016/j.gene.2014.05.043. View

19.

Lang J, Darling A, Eisen J . Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices. PLoS One. 2013; 8(4):e62510. PMC: 3636077. DOI: 10.1371/journal.pone.0062510. View

20.

Jiang B, Song K, Ren J, Deng M, Sun F, Zhang X . Comparison of metagenomic samples using sequence signatures. BMC Genomics. 2012; 13:730. PMC: 3549735. DOI: 10.1186/1471-2164-13-730. View