The evolution of domain-content in bacterial genomes

Nacho Molina,Erik Van Nimwegen

doi:10.1186/1745-6150-3-51

Nacho Molina, Erik Van Nimwegen

Open Access

https://doi.org/10.1186/1745-6150-3-51

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Abstract

BackgroundAcross all sequenced bacterial genomes, the number of domains nc in different functional categories c scales as a power-law in the total number of domains n, i.e. , with exponents αc 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.ResultsWe 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 nc 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 nc, the rate of additions and deletions of domains of category c is proportional to a category-dependent constant ρc, which is the same for all evolutionary lineages. This 'evolutionary potential' ρc 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 αc. 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.ConclusionOur 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.ReviewersThis article was reviewed by Eugene V. Koonin, Martijn A. Huynen, and Sergei Maslov.

Highlights

Across all sequenced bacterial genomes, the number of domains nc in different functional categories c scales as a power-law in the total number of domains n, i.e. nc ∝ nac, with exponents αc that vary across functional categories
Biology Direct 2008, 3:51 http://www.biology-direct.com/content/3/1/51 facto null model of sequence evolution and the availability of such a null model was crucial for the development of rigorous methods for reconstructing evolutionary phylogenies (e.g. [4]) and methods for detecting selection acting on gene sequences (e.g. [5,6])
Across all bacteria and for most highlevel GO categories c, the number of domain occurrences nc scales as a power-law in the total number of domains n, with scaling exponents αc varying from close to zero to a bit larger than 2

Summary

Introduction

Across all sequenced bacterial genomes, the number of domains nc in different functional categories c scales as a power-law in the total number of domains n, i.e. nc ∝ nac , with exponents αc that vary across functional categories. The inferred rate of amino acid substitutions was so high that it was hard to imagine how all of these substitutions could have been fixed by the action of natural selection [2] This famously lead Kimura to propose the neutral theory of molecular evolution [3]. The scaling laws are time invariant, we derive a 'null model' for genome evolution that accounts for the observed scaling laws. In this model the exponents of the scaling laws are identified as universal constants of the evolutionary process

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