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Deposited research article

Universality in large-scale structure of complete genomes

Li-Ching Hsieh^1,2, Ta-Yuan Chen¹, Chang-Heng Chang¹, Wen-Lang Fan¹ and Hoong-Chien Lee^1,2,3

¹  Department of Physics, National Central University, Chungli, Taiwan 320

²  Department of Life Sciences, National Central University, Chungli, Taiwan 320.

³  Center for Complex Systems, National Central University, Chungli, Taiwan 320

author email corresponding author email

Genome Biology 2004, 5:P7doi:10.1186/gb-2004-5-3-p7

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

Subject areas: Evolution, Genome studies, Bioinformatics

The electronic version of this article is the complete one and can be found online at: http://genomebiology.com/2004/5/3/P7

Received:	26 January 2004
Posted:	28 January 2004

© 2004 BioMed Central Ltd

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.

Deposited research article

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