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Conservation versus variation of dinucleotide frequencies across genomes: Evolutionary implications

Shang-Hong Zhang* and Jian-Hua Yang

Author Affiliations

The Key Laboratory of Gene Engineering of Ministry of Education, and Biotechnology Research Center, Sun Yat-Sen University, Guangzhou 510275, China.

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Genome Biology 2005, 6:P12  doi:10.1186/gb-2005-6-11-p12

This was the first version of this article to be made available publicly.

The electronic version of this article is the complete one and can be found online at:

Received:6 October 2005
Published:11 October 2005

© 2005 BioMed Central Ltd



In order to find traits or evolutionary relics of the primordial genome (the most primitive nucleic acid genome for earth's life) remained in modern genomes, we have studied the characteristics of dinucleotide frequencies across genomes. As the longer a sequence is, the more probable it would be modified during genome evolution. For that reason, short nucleotide sequences, especially dinucleotides, would have considerable chances to be intact during billions of years of evolution. Consequently, conservation of the genomic profiles of the frequencies of dinucleotides across modern genomes may exist and would be an evolutionary relic of the primordial genome.


Based on this assumption, we analyzed the frequency profiles of dinucleotides of the whole-genome sequences from 130 prokaryotic species (including archaea and bacteria). The statistical results show that the frequencies of the dinucleotides AC, AG, CA, CT, GA, GT, TC, and TG are well conserved across genomes, while the frequencies of other dinucleotides vary considerably among species. This conservation/variation seems to be linked to the distributions of dinucleotides throughout a genome and across genomes, and also to have relation to strand symmetry.


We argue and conclude that the phenomenon of frequency conservation would be evolutionary relics of the primordial genome, which may provide insights into the study of the origin and evolution of genomes.

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