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Universality in large-scale structure of complete genomes

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.

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Correspondence to Hoong-Chien Lee.

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Hsieh, LC., Chen, TY., Chang, CH. et al. Universality in large-scale structure of complete genomes. Genome Biol 5, P7 (2004). https://doi.org/10.1186/gb-2004-5-3-p7

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Keywords

  • Plasmodium
  • Complete Genome
  • Spectral Width
  • Universality Class
  • Neutral Theory