Working PaperArticleVersion 1This version is not peer-reviewed
Visualizing the Echo of Evolution: Tandem Repeats and Sequence Structure of Chromosomes of Saccharomyces cerevisiae shown by Doublet Frequency Distance Maps
Version 1
: Received: 30 July 2021 / Approved: 6 August 2021 / Online: 6 August 2021 (14:25:42 CEST)
How to cite:
Köhler, J.M. Visualizing the Echo of Evolution: Tandem Repeats and Sequence Structure of Chromosomes of Saccharomyces cerevisiae shown by Doublet Frequency Distance Maps. Preprints2021, 2021080170
Köhler, J.M. Visualizing the Echo of Evolution: Tandem Repeats and Sequence Structure of Chromosomes of Saccharomyces cerevisiae shown by Doublet Frequency Distance Maps. Preprints 2021, 2021080170
Cite as:
Köhler, J.M. Visualizing the Echo of Evolution: Tandem Repeats and Sequence Structure of Chromosomes of Saccharomyces cerevisiae shown by Doublet Frequency Distance Maps. Preprints2021, 2021080170
Köhler, J.M. Visualizing the Echo of Evolution: Tandem Repeats and Sequence Structure of Chromosomes of Saccharomyces cerevisiae shown by Doublet Frequency Distance Maps. Preprints 2021, 2021080170
Abstract
The method of doublet frequency distance (DFD-) maps was applied, here, for visualization of DNA sequence structures of yeast chromosomes. The colour scale “rainbow” of the Octave programming tool is well suited for such visualization. The DFD-maps are generated by comparison of the differences in the number of all base doublets in a shifting frame with all other positions of this frame in a regarded DNA sequence section. This procedure can be applied from DNA-sections of between a few hundred bases (bps) up to a complete chromosome with a million or more bps. An orthogonal DFD-map pattern dominates all chromosomes and its parts. It can be interpreted by a large number of successive mutation events during evolution. In contrast, diagonal patterns indicate duplications of sequence sections and multiple tandem repeats. These periodic structures are found in several chromosomes and are more or less regular or noised. The larger tandem repeat in the subtelomeric region of chromosome 12 presents a characteristic example of a nested multiple-repeat structure. Its pattern in the DFD-map illustrates obviously a temporal order of duplication and mutation events leading to a hierarchical sequence architecture.
Keywords
DNA; Chromosomes; Yeast; Tandem Repeats; Evolution; Genetic Noise; Visualization; Doublet Frequency Maps; Sequence structure
Subject
LIFE SCIENCES, Genetics
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
