Gaussian-Distributed Codon Frequencies of Genomes

G3: Genes, Genomes, Genetics

Bohdan B. Khomtchouk^1¹  Wolfgang Nonner^2² 

[1] Department of Biology, Stanford University, Stanford, CA 94305^1;Department of Physiology and Biophysics, University of Miami Miller School of Medicine, Miami, FL 33136^2

关键词: evolution;    genomics;    codon usage;    genetic code;   

DOI  :  10.1534/g3.118.200939

学科分类：生物科学（综合）

来源: Genetics Society of America

【 摘 要 】

DNA encodes protein primary structure using 64 different codons to specify 20 different amino acids and a stop signal. Frequencies of codon occurrence when ordered in descending sequence provide a global characterization of a genome’s preference (bias) for using the different codons of the redundant genetic code. Whereas frequency/rank relations have been described by empirical expressions, here we propose a statistical model in which two different forms of codon usage co-exist in a genome. We investigate whether such a model can account for the range of codon usages observed in a large set of genomes from different taxa. The differences in frequency/rank relations across these genomes can be expressed in a single parameter, the proportion of the two codon compartments. One compartment uses different codons with weak bias according to a Gaussian distribution of frequency, the other uses different codons with strong bias. In prokaryotic genomes both compartments appear to be present in a wide range of proportions, whereas in eukaryotic genomes the compartment with Gaussian distribution tends to dominate. Codon frequencies that are Gaussian-distributed suggest that many evolutionary conditions are involved in shaping weakly-biased codon usage, whereas strong bias in codon usage suggests dominance of few evolutionary conditions.

【 授权许可】

CC BY