Genome sizes and the Benford distribution

• Published in: PloS one 2012-05, Vol.7 (5), p.e36624-e36624
• Main Authors: Friar, James L, Goldman, Terrance, Pérez-Mercader, Juan
• Format: Article
• Language: English
• Subjects: Animals; Archaea - genetics; Bacteria - genetics; Biology; Communication; Distribution functions; Entropy; ENVIRONMENTAL SCIENCES; Eukaryota - genetics; Eukaryotes; Evolution; Evolution, Molecular; Functions (mathematics); Genes; Genome; Genome Size; Genomes; Genomics; Information processing; Information theory; Laboratories; Mathematics; Mycoplasma genitalium; Open Reading Frames; Physics; Probability distribution; Probability distribution functions; Probability distributions; Prokaryotes; Proteins; Science & Technology - Other Topics
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0036624

Data on the number of Open Reading Frames (ORFs) coded by genomes from the 3 domains of Life show the presence of some notable general features. These include essential differences between the Prokaryotes and Eukaryotes, with the number of ORFs growing linearly with total genome size for the former, but only logarithmically for the latter. Simply by assuming that the (protein) coding and non-coding fractions of the genome must have different dynamics and that the non-coding fraction must be particularly versatile and therefore be controlled by a variety of (unspecified) probability distribution functions (pdf's), we are able to predict that the number of ORFs for Eukaryotes follows a Benford distribution and must therefore have a specific logarithmic form. Using the data for the 1000+ genomes available to us in early 2010, we find that the Benford distribution provides excellent fits to the data over several orders of magnitude. In its linear regime the Benford distribution produces excellent fits to the Prokaryote data, while the full non-linear form of the distribution similarly provides an excellent fit to the Eukaryote data. Furthermore, in their region of overlap the salient features are statistically congruent. This allows us to interpret the difference between Prokaryotes and Eukaryotes as the manifestation of the increased demand in the biological functions required for the larger Eukaryotes, to estimate some minimal genome sizes, and to predict a maximal Prokaryote genome size on the order of 8-12 megabasepairs. These results naturally allow a mathematical interpretation in terms of maximal entropy and, therefore, most efficient information transmission.