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Deposited research article

Increasing biological complexity is positively correlated with the relative genome-wide expansion of non-protein-coding DNA sequences

Ryan J Taft13* and John S Mattick2

Author Affiliations

1 Rowe Program in Genetics, Department of Biological Chemistry, University of California, Davis, School of Medicine

2 ARC Special Research Centre for Functional and Applied Genomics, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia

3 Current address: California Pacific Medical Center Research Institute 2330 Clay St., San Francisco, CA 94115

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Genome Biology 2003, 5:P1  doi:10.1186/gb-2003-5-1-p1


This was the first version of this article to be made available publicly. This article was submitted to Genome Biology for peer review.

The electronic version of this article is the complete one and can be found online at: http://genomebiology.com/2003/5/1/P1


Received:24 November 2003
Published:1 December 2003

© 2003 BioMed Central Ltd

Abstract

Background

Prior to the current genomic era it was suggested that the number of protein-coding genes that an organism made use of was a valid measure of its complexity. It is now clear, however, that major incongruities exist and that there is only a weak relationship between biological complexity and the number of protein coding genes. For example, using the protein-coding gene number as a basis for evaluating biological complexity would make urochordates and insects less complex than nematodes, and humans less complex than rice.

Results

We analyzed the ratio of noncoding to total genomic DNA (ncDNA/tgDNA) for 85 sequenced species and found that this ratio correlates well with increasing biological complexity. The ncDNA/tgDNA ratio is generally contained within the bandwidth of 0.05 - 0.24 for prokaryotes, but rises to 0.26 - 0.52 in unicellular eukaryotes, and to 0.62 - 0.985 for developmentally complex multicellular organisms. Significantly, prokaryotic species display a non-uniform species distribution approaching the mean of 0.1177 ncDNA/tgDNA (p = 1.58 x 10-13), and a nonlinear ncDNA/tgDNA relationship to genome size (r = 0.15). Importantly, the ncDNA/tgDNA ratio corrects for ploidy, and is not substantially affected by variable loads of repetitive sequences.

Conclusions

We suggest that the observed noncoding DNA increases and compositional patterns are primarily a function of increased information content. It is therefore possible that introns, intergenic sequences, repeat elements, and genomic DNA previously regarded as genetically inert may be far more important to the evolution and functional repertoire of complex organisms than has been previously appreciated.

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