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Updated: May 15, 2026

An Integrated Approach for Microprotein Identification and Sequence Analysis

An Integrated Approach for Microprotein Identification and Sequence Analysis

Published on: July 12, 2022

Evolution of coding microsatellites in primate genomes.

Etienne Loire¹, Dominique Higuet, Pierre Netter

¹UMR 7138, Systématique, Adaptation, Evolution (UPMC, CNRS, MNHN, IRD), Paris, France.

Genome Biology and Evolution

|January 15, 2013

Summary

This summary is machine-generated.

Genomic coding regions unexpectedly contain many simple sequence repeats (SSRs). Despite their potential to cause frameshifts, SSRs in primate genes evolve primarily through substitutions, suggesting a balance between mutation and selection.

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Area of Science:

Comparative genomics
Molecular evolution
Population genetics

Background:

Simple sequence repeats (SSRs) are prone to length changes (expansions/contractions).
SSRs in coding sequences can cause frameshifts, implying strong negative selection.
Despite this, coding sequences harbor numerous SSRs across various types.

Purpose of the Study:

Investigate the evolutionary dynamics of SSRs within coding regions across primate species.
Determine the primary mechanisms driving SSR evolution in coding sequences.
Assess the selective pressures acting on coding SSRs and their relationship to gene function.

Main Methods:

Phylogenetic analysis of orthologous genes in human, chimpanzee, orangutan, and macaque genomes.
Identification and classification of SSRs (mono-, di-, tri-, tetra-, hexa-nucleotide) within coding sequences.
Quantification of SSR evolution via substitutions, insertions, and deletions.
Estimation of fitness costs associated with coding mono-SSRs.

Main Results:

SSRs in coding regions, excluding tri- and hexa-SSRs, predominantly evolve through substitutions.
Substitution rates for all coding SSR types are approximately double those of the surrounding coding sequences.
Despite continuous creation and loss, the overall number of coding SSRs remains stable, indicating equilibrium.
The fitness cost of coding mono-SSRs increases with repeat unit number and varies significantly with gene function.

Conclusions:

Coding SSRs are maintained by a balance of mutation, genetic drift, and selection.
Gene function influences the strength of selection against coding SSRs.
The observed equilibrium suggests functional constraints on SSR evolution within coding regions.