  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.

Genomics;Populations and Evolution