Genome Biology

, 5:P7 | Cite as

Universality in large-scale structure of complete genomes

  • Li-Ching Hsieh
  • Ta-Yuan Chen
  • Chang-Heng Chang
  • Wen-Lang Fan
  • Hoong-Chien Lee
Deposited research article

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.

Keywords

Plasmodium Complete Genome Spectral Width Universality Class Neutral Theory 

Copyright information

© BioMed Central Ltd 2004

Authors and Affiliations

  • Li-Ching Hsieh
    • 1
    • 2
  • Ta-Yuan Chen
    • 1
  • Chang-Heng Chang
    • 1
  • Wen-Lang Fan
    • 1
  • Hoong-Chien Lee
    • 1
    • 2
    • 3
  1. 1.Department of PhysicsNational Central UniversityChungli
  2. 2.Department of Life SciencesNational Central UniversityChungliTaiwan
  3. 3.Center for Complex SystemsNational Central UniversityChungliTaiwan

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