Abstract
AbstractOne of the objectives of evolutionary genomics is to reveal the genetic information contained in the primordial genome (called the primary genetic information in this paper, with the primordial genome defined here as the most primitive nucleic acid genome for earth’s life) by searching for primitive traits or relics remained in modern genomes. As the shorter a sequence is, the less probable it would be modified during genome evolution. For that reason, some characteristics of very short nucleotide sequences would have considerable chances to persist during billions of years of evolution. Consequently, conservation of certain genomic features of mononucleotides, dinucleotides, and higher-order oligonucleotides across various genomes may exist; some, if not all, of these features would be relics of the primary genetic information. Based on this assumption, we analyzed the pattern of frequencies of mononucleotides, dinucleotides, and higher-order oligonucleotides of the whole-genome sequences from 458 species (including archaea, bacteria, and eukaryotes). Also, we studied the phenomenon of strand symmetry in these genomes. The results show that the conservation of frequencies of some dinucleotides and higher-order oligonucleotides across genomes does exist, and that strand symmetry is a ubiquitous and explicit phenomenon that may contribute to frequency conservation. We propose a new hypothesis for the origin of strand symmetry and frequency conservation as well as for the constitution of early genomes. We conclude that the phenomena of strand symmetry and the pattern of frequency conservation would be original features of the primary genetic information.
Highlights
In the course of billions of years of evolution, organic genomes have undergone enormous changes
The results show that the conservation of frequencies of some dinucleotides and higher-order oligonucleotides across genomes does exist, and that strand symmetry is a ubiquitous and explicit phenomenon contributing to this conservation
Given that the frequencies of a dinucleotide are conserved across genomes, so are those of its reverse complement, which is consistent with the phenomenon of strand symmetry
Summary
In the course of billions of years of evolution, organic genomes have undergone enormous changes. If a considerable proportion (the number of copies) of a very short sequence has not been modified by nucleotide substitutions, insertions or deletions in evolving genomes, and/or if the variation of its occurrence frequencies has been limited by a certain mechanism (system) since the beginning or early stages of genome evolution, the pattern of genomic frequencies of the sequence would be conserved throughout the time, i.e., no significant changes since the primordial genome formed From this point forward, our philosophy suggests that the conservation of the genomic pattern of the frequencies of mononucleotides, dinucleotides, and higher-order oligonucleotides across various genomes, if it exists, would probably be a relic of the primordial genome
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