gb-2004-5-3-p7 GBJ Deposited research article <p>Universality in large-scale structure of complete genomes</p> Hsieh Li-Ching Chen Ta-Yuan Chang Chang-Heng Fan Wen-Lang Lee Hoong-Chien hclee@phy.ncu.edu.tw

Department of Physics, National Central University, Chungli, Taiwan 320

Department of Life Sciences, National Central University, Chungli, Taiwan 320.

Center for Complex Systems, National Central University, Chungli, Taiwan 320

 Genome Biology 1465-6906 2004 5 3 P7 http://genomebiology.com/2004/5/3/P7 This is the first version of this article to be made available publicly. 10.1186/gb-2004-5-3-p7 26 1 2004 28 1 2004 2004 BioMed Central Ltd

Our analysis of occurrence frequencies of short oligonucleotides in all extant complete genomes suggests that ancestral genomes grew via a mechanism whose main components were neutral stochastic segmental replicative translocations and random small mutations.

Abstract

The abundance of duplications in genomes in the form of paralogs, pseudogenes and a variety of repeats suggests that genomes may have used duplications as one mode for their growth. However a systematic knowledge on all possible duplications in whole genomes is still lacking. This paper reports the results of a detailed study of occurrence frequencies of short oligonucleotides in all extant complete genomes. We found a systematic pattern of repeats of short oligonucleotides that places all the complete genomes except Plasmodium in a single universality class expressed by an extremely simple formula. Our analysis of the data combined with computer simulation of genome growth models suggest a simple coarse-grain representation of genome growth: the ancestors of the genomes began to grow when they were no greater than 300 b in length via a mechanism whose main components were neutral stochastic segmental replicative translocations and random small mutations.

 Evolution Genome studies Bioinformatics