Function Overcomes Taxonomy for Organella Genes Triplet Composition

Michael Sadovsky; Maria Yu Senashova; Olga Mutovina; Anna A Molyavko; Viktoria D Fedotovskaya; Tatiana Shpagina; Yana Nedorez; Yulia Putintseva

doi:10.20944/preprints202201.0425.v1

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preprints.org > life sciences > molecular biology > doi: 10.20944/preprints202201.0425.v1

Preprint Article Version 1 Preserved in Portico This version is not peer-reviewed

Function Overcomes Taxonomy for Organella Genes Triplet Composition

^* ,

Viktoria D Fedotovskaya

Tatiana Shpagina

Yana Nedorez

Yulia Putintseva

Version 1 : Received: 25 January 2022 / Approved: 27 January 2022 / Online: 27 January 2022 (17:40:07 CET)

How to cite: Sadovsky, M.; Senashova, M.Y.; Mutovina, O.; Molyavko, A.A.; Fedotovskaya, V.D.; Shpagina, T.; Nedorez, Y.; Putintseva, Y. Function Overcomes Taxonomy for Organella Genes Triplet Composition. Preprints 2022, 2022010425. https://doi.org/10.20944/preprints202201.0425.v1. Sadovsky, M.; Senashova, M.Y.; Mutovina, O.; Molyavko, A.A.; Fedotovskaya, V.D.; Shpagina, T.; Nedorez, Y.; Putintseva, Y. Function Overcomes Taxonomy for Organella Genes Triplet Composition. Preprints 2022, 2022010425. https://doi.org/10.20944/preprints202201.0425.v1.

Cite as:

Sadovsky, M.; Senashova, M.Y.; Mutovina, O.; Molyavko, A.A.; Fedotovskaya, V.D.; Shpagina, T.; Nedorez, Y.; Putintseva, Y. Function Overcomes Taxonomy for Organella Genes Triplet Composition. Preprints 2022, 2022010425. https://doi.org/10.20944/preprints202201.0425.v1. Sadovsky, M.; Senashova, M.Y.; Mutovina, O.; Molyavko, A.A.; Fedotovskaya, V.D.; Shpagina, T.; Nedorez, Y.; Putintseva, Y. Function Overcomes Taxonomy for Organella Genes Triplet Composition. Preprints 2022, 2022010425. https://doi.org/10.20944/preprints202201.0425.v1.

Abstract

A comprehensive presentation of a variety of biologically sounding properties of genomes is present; chloroplast genomes are used as a biological matter. Triplet frequency composition is the general issue standing behind the properties. Besides, the new alignment-free error-tolerant method of sequences comparison highly efficient for in/del mismatches is present, for transposons search. Triplet frequency dictionaries determined for a genome, or for a part of that latter were studied through various clustering techniques. The interplay between triplet composition and function reveals on tRNA genes unambiguously shows the prevalence of the function encoded in tRNA gene over the phylogeny: the genes gather into the clusters comprising the genes encoding the same amino acid; more exactly, few gene families exhibit fine cluster pattern corresponding the synonymous codons of amino acid. Previously reported symmetry in chloroplast genomes is shown for a set of gymnosperm: that is mirror symmetry, rotational symmetry, and the second Chargaff's parity rule asymmetry. A family of transposons was found in gymnosperm chloroplast genomes. This family is revealed through the novel comparison method based on convolution calculation, for a set of DNA sequences.

Keywords

transposon; order; triplet frequency; tRNA; clustering; taxonomy; symmetry; photosystem

Subject

LIFE SCIENCES, Molecular Biology

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.

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