Abstract
During the long history of biological evolution, genome structures have undergone enormous changes. Nevertheless, some traits or vestiges of the primordial genome (defined as the most primitive nucleic acid genome for life on earth in this paper) may remain in modern genetic systems. It is of great importance to find these traits or vestiges for the study of the origin and evolution of genomes. As the shorter is a sequence, the less probable it would be modified during genome evolution. And if mutated, it would be easier to reappear at the same site or another site. Consequently, the genomic frequencies of very short nucleotide sequences, such as dinucleotides, would have considerable chances to be conserved during billions of years of evolution. Prokaryotic genomes are very diverse and with a wide range of GC content. Therefore, in order to find traits or vestiges of the primordial genome remained in modern genetic systems, we have studied the characteristics of dinucleotide frequencies across bacterial and archaeal genomes. We analyzed the dinucleotide frequency patterns of the whole-genome sequences from more than 1300 prokaryotic species (bacterial and archaeal genomes available as of December 2012). The results show that the frequencies of the dinucleotides AC, AG, CA, CT, GA, GT, TC, and TG are well-conserved across various genomes, while the frequencies of other dinucleotides vary considerably among species. The dinucleotide frequency conservation/variation pattern seems to correlate with the distributions of dinucleotides throughout a genome and across genomes. Further analysis indicates that the phenomenon would be determined by strand symmetry of genomic sequences (the second parity rule) and GC content variations among genomes. We discussed some possible origins of strand symmetry. And we propose that the phenomenon of frequency conservation of some dinucleotides may provide insights into the genomic composition of the primordial genetic system.
Highlights
During billions of years of evolution, organic genomes have undergone enormous changes
We propose that the frequency conservation patterns would be vestiges of the primordial genome, considering that the phenomenon would depend on strand symmetry of genomic sequences and on GC content variations among genomes
The frequencies of mononucleotides vary greatly, from 13.5 to 74.9% in terms of GC content, among genomes in our study (Figure 1). This variation of GC content among genomes is on the whole similar to the distribution of genomic GC content for prokaryotic species with whole-genome sequences available as of December 2008 (Zhang and Wang, 2011)
Summary
During billions of years of evolution, organic genomes have undergone enormous changes. Our philosophy suggests that if the frequencies of a dinucleotide in modern genomes are conserved, it would imply that the genomic frequencies of that particular dinucleotide have not changed significantly since the primordial genome formed, a vestige of the primordial genome. Based on this assumption, comparative analysis of the characteristics of dinucleotides in the genomes of various organisms may provide insights into the features of the primordial genome as well as the primary genetic information it contained
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
