SMILE

Stochastic Models for the Inference of Life Evolution

Evolution of coding microsatellites in primate genomes

Loire, E., Higuet, D., Netter, P., Achaz, G.

Genome Biology and Evolution

2013

Microsatellites (SSRs) are highly susceptible to expansions and contractions. When located in a coding sequence, the insertion or the deletion of a single unit for a mono-, di-, tetra-, or penta(nucleotide)-SSR creates a frameshift. As a consequence, one would expect to find only very few of these SSRs in coding sequences because of their strong deleterious potential. Unexpectedly, genomes contain many coding SSRs of all types. Here, we report on a study of their evolution in a phylogenetic context using the genomes of four primates: human, chimpanzee, orangutan, and macaque. In a set of 5,015 orthologous genes unambiguously aligned among the four species, we show that, except for tri- and hexa-SSRs, for which insertions and deletions are frequently observed, SSRs in coding regions evolve mainly by substitutions. We show that the rate of substitution in all types of coding SSRs is typically two times higher than in the rest of coding sequences. Additionally, we observe that although numerous coding SSRs are created and lost by substitutions in the lineages, their numbers remain constant. This last observation suggests that the coding SSRs have reached equilibrium. We hypothesize that this equilibrium involves a combination of mutation, drift, and selection. We thus estimated the fitness cost of mono-SSRs and show that it increases with the number of units. We finally show that the cost of coding mono-SSRs greatly varies from function to function, suggesting that the strength of the selection that acts against them can be correlated to gene functions.

Bibtex

@article{loire_evolution_2013,
Author = {Loire, Etienne and Higuet, Dominique and Netter,
Pierre and Achaz, Guillaume},
Title = {Evolution of coding microsatellites in primate genomes},
Journal = {Genome Biology and Evolution},
Volume = {5},
Number = {2},
Pages = {283--295},
abstract = {Microsatellites (SSRs) are highly susceptible to
expansions and contractions. When located in a coding
sequence, the insertion or the deletion of a single
unit for a mono-, di-, tetra-, or penta(nucleotide)-SSR
creates a frameshift. As a consequence, one would
expect to find only very few of these SSRs in coding
sequences because of their strong deleterious
potential. Unexpectedly, genomes contain many coding
SSRs of all types. Here, we report on a study of their
evolution in a phylogenetic context using the genomes
of four primates: human, chimpanzee, orangutan, and
macaque. In a set of 5,015 orthologous genes
unambiguously aligned among the four species, we show
that, except for tri- and hexa-SSRs, for which
insertions and deletions are frequently observed, SSRs
in coding regions evolve mainly by substitutions. We
show that the rate of substitution in all types of
coding SSRs is typically two times higher than in the
rest of coding sequences. Additionally, we observe that
although numerous coding SSRs are created and lost by
substitutions in the lineages, their numbers remain
constant. This last observation suggests that the
coding SSRs have reached equilibrium. We hypothesize
that this equilibrium involves a combination of
mutation, drift, and selection. We thus estimated the
fitness cost of mono-SSRs and show that it increases
with the number of units. We finally show that the cost
of coding mono-SSRs greatly varies from function to
function, suggesting that the strength of the selection
that acts against them can be correlated to gene
functions.},
doi = {10.1093/gbe/evt003},
issn = {1759-6653},
language = {eng},
pmcid = {PMC3590770},
pmid = {23315383},
year = 2013
}

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