ArticleNucleic acids research2012
Evolutionary pressures on simple sequence repeats in prokaryotic coding regions.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed.
- Comparative Genomic Analysis of Coding Sequence-Derived Microsatellites Reveals Evolutionary Conservation and Genetic Diversity in Forest Musk Deer (Veterinary sciences · 2026Article
- GBSC: graph-based sequence clustering method for similar short tandem repeats in protein sequences.Bioinformatics (Oxford, England) · 2026Article
- CB-Search: a method for searching for similar protein motifs with biased compositions.BMC bioinformatics · 2026Article
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- Fit for purpose: evaluation and evolution of agricultural bioinoculants across production landscapes.ISME communications · 2026Review
- The repertoire of short tandem repeats across the tree of life.Genome biology · 2025Article
- AI-directed gene fusing prolongs the evolutionary half-life of synthetic gene circuits.Science advances · 2025Article
- Accurate detection of tandem repeats exposes ubiquitous reuse of biological sequences.Nucleic acids research · 2025Article
- Pathogen contingency loci and the evolution of host specificity: Simple sequence repeats mediate Bartonella adaptation to a wild rodent host.PLoS pathogens · 2024Article
- Development and Application of Potentially Universal Microsatellite Markers for Pheasant Species.Animals : an open access journal from MDPI · 2023Article
- Development of Simple Sequence Repeat Markers and Genetic Diversity Evaluation ofJournal of fungi (Basel, Switzerland) · 2023Article
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- Comparison of microsatellite distribution in the genomes of Pteropus vampyrus and Miniopterus natalensis (Chiroptera).BMC genomic data · 2023Article
- Comprehensive Comparative Analysis Sheds Light on the Patterns of Microsatellite Distribution across Birds Based on the Chromosome-Level Genomes.Animals : an open access journal from MDPI · 2023Article
- Complete Chloroplast Genomes of 14 Subspecies ofGenes · 2022Article
- Evolutionary Stability Optimizer (ESO): A Novel Approach to Identify and Avoid Mutational Hotspots in DNA Sequences While Maintaining High Expression Levels.ACS synthetic biology · 2022Article
- Two short low complexity regions (LCRs) are hallmark sequences of the Delta SARS-CoV-2 variant spike protein.Scientific reports · 2022Article
- Occurrence of simple sequence repeats in cDNA sequences of safflower (Frontiers in plant science · 2022Article
- Comparative genomic study on the complete plastomes of four officinal Ardisia species in China.Scientific reports · 2021Article
- Evolution of Pseudomonas aeruginosa toward higher fitness under standard laboratory conditions.The ISME journal · 2021Article
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2 authors.
Funding
Abstract
Simple sequence repeats (SSRs) are indel mutational hotspots in genomes. In prokaryotes, SSR loci can cause phase variation, a microbial survival strategy that relies on stochastic, reversible on-off switching of gene activity. By analyzing multiple strains of 42 fully sequenced prokaryotic species, we measure the relative variability and density distribution of SSRs in coding regions. We demonstrate that repeat type strongly influences indel mutation rates, and that the most mutable types are most strongly avoided across genomes. We thoroughly characterize SSR density and variability as a function of N→C position along protein sequences. Using codon-shuffling algorithms that preserve amino acid sequence, we assess evolutionary pressures on SSRs. We find that coding sequences suppress repeats in the middle of proteins, and enrich repeats near termini, yielding U-shaped SSR density curves. We show that for many species this characteristic shape can be attributed to purely biophysical constraints of protein structure. In multiple cases, however, particularly in certain pathogenic bacteria, we observe over enrichment of SSRs near protein N-termini significantly beyond expectation based on structural constraints. This increases the probability that frameshifts result in non-functional proteins, revealing that these species may evolutionarily tune SSR positions in coding regions to facilitate phase variation.
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