Research

The evolution of domain-content in bacterial genomes

Nacho Molina and Erik van Nimwegen

Biozentrum, University of Basel, and Swiss Institute of Bioinformatics Klingelbergstrasse 50/70, 4056-CH, Basel, Switzerland

author email corresponding author email

Biology Direct 2008, 3:51doi:10.1186/1745-6150-3-51

Published:	11 December 2008

Abstract

Background

Across all sequenced bacterial genomes, the number of domains n_c in different functional categories c scales as a power-law in the total number of domains n, i.e. , with exponents α_c that vary across functional categories. Here we investigate the implications of these scaling laws for the evolution of domain-content in bacterial genomes and derive the simplest evolutionary model consistent with these scaling laws.

Results

We show that, using only an assumption of time invariance, the scaling laws uniquely determine the relative rates of domain additions and deletions across all functional categories and evolutionary lineages. In particular, the model predicts that the rate of additions and deletions of domains of category c is proportional to the number of domains n_c currently in the genome and we discuss the implications of this observation for the role of horizontal transfer in genome evolution. Second, in addition to being proportional to n_c, the rate of additions and deletions of domains of category c is proportional to a category-dependent constant ρ_c, which is the same for all evolutionary lineages. This 'evolutionary potential' ρ_c represents the relative probability for additions/deletions of domains of category c to be fixed in the population by selection and is predicted to equal the scaling exponent α_c. By comparing the domain content of 93 pairs of closely-related genomes from all over the phylogenetic tree of bacteria, we demonstrate that the model's predictions are supported by available genome-sequence data.

Conclusion

Our results establish a direct quantitative connection between the scaling of domain numbers with genome size, and the rate of addition and deletions of domains during short evolutionary time intervals.

Reviewers

This article was reviewed by Eugene V. Koonin, Martijn A. Huynen, and Sergei Maslov.