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Deletion Rate Evolution and Its Effect on Genome Size and Coding Density

Pettersson, Mats E.; Kurland, Charles LU and Berg, Otto G. (2009) In Molecular Biology and Evolution 26(6). p.1421-1430
Abstract
Deletion rates are thought to be important factors in determining the genome size of organisms in nature. Although it is indisputable that deletions, and thus deletion rates, affect genome size, it is unclear how, or indeed if, genome size is regulated via the deletion rate. Here, we employ a mathematical model to determine the evolutionary fate of deletion rate mutants. Simulations are employed to explore the interactions between deletions, deletion rate mutants, and genome size. The results show that, in this model, the fate of deletion rate mutants will depend on the fraction of essential genomic material, on the frequency of sexual recombination, as well as on the population size of the organism. We find that there is no optimal... (More)
Deletion rates are thought to be important factors in determining the genome size of organisms in nature. Although it is indisputable that deletions, and thus deletion rates, affect genome size, it is unclear how, or indeed if, genome size is regulated via the deletion rate. Here, we employ a mathematical model to determine the evolutionary fate of deletion rate mutants. Simulations are employed to explore the interactions between deletions, deletion rate mutants, and genome size. The results show that, in this model, the fate of deletion rate mutants will depend on the fraction of essential genomic material, on the frequency of sexual recombination, as well as on the population size of the organism. We find that there is no optimal deletion rate in any state. However, at one critical coding density, all changes in deletion rate are neutral and the rate may drift either up or down. As a consequence, the coding density of the genome is expected to fluctuate around this critical density. Characteristic differences in the impact of deletion rate mutations on prokaryote and eukaryote genomes are described. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
modifier evolution, deletion bias, insertion-deletion dynamics, genome size, junk DNA
in
Molecular Biology and Evolution
volume
26
issue
6
pages
1421 - 1430
publisher
Oxford University Press
external identifiers
  • wos:000266116500018
  • scopus:66249117322
ISSN
0737-4038
DOI
10.1093/molbev/msp054
language
English
LU publication?
yes
id
37d0a7af-7f9b-4d5e-8afc-bf4ef9a70233 (old id 1425586)
date added to LUP
2009-07-01 15:01:02
date last changed
2017-06-04 03:45:23
@article{37d0a7af-7f9b-4d5e-8afc-bf4ef9a70233,
  abstract     = {Deletion rates are thought to be important factors in determining the genome size of organisms in nature. Although it is indisputable that deletions, and thus deletion rates, affect genome size, it is unclear how, or indeed if, genome size is regulated via the deletion rate. Here, we employ a mathematical model to determine the evolutionary fate of deletion rate mutants. Simulations are employed to explore the interactions between deletions, deletion rate mutants, and genome size. The results show that, in this model, the fate of deletion rate mutants will depend on the fraction of essential genomic material, on the frequency of sexual recombination, as well as on the population size of the organism. We find that there is no optimal deletion rate in any state. However, at one critical coding density, all changes in deletion rate are neutral and the rate may drift either up or down. As a consequence, the coding density of the genome is expected to fluctuate around this critical density. Characteristic differences in the impact of deletion rate mutations on prokaryote and eukaryote genomes are described.},
  author       = {Pettersson, Mats E. and Kurland, Charles and Berg, Otto G.},
  issn         = {0737-4038},
  keyword      = {modifier evolution,deletion bias,insertion-deletion dynamics,genome size,junk DNA},
  language     = {eng},
  number       = {6},
  pages        = {1421--1430},
  publisher    = {Oxford University Press},
  series       = {Molecular Biology and Evolution},
  title        = {Deletion Rate Evolution and Its Effect on Genome Size and Coding Density},
  url          = {http://dx.doi.org/10.1093/molbev/msp054},
  volume       = {26},
  year         = {2009},
}