ArticleBMC genomics2021
Genome-wide characterization of microsatellite DNA in fishes: survey and analysis of their abundance and frequency in genome-specific regions.
Article in BMC genomics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 50 citations in OpenAlex.
- Pan-SSR architecture in Acrossocheilus fasciatus links cross-assembly repeat conservation, repeat-unit count variation, and genomic context.Molecular genetics and genomics : MGG · 2026Article
- Genomic distribution characteristics and interspecific differences of microsatellite landscapes in Felidae.BMC genomics · 2026Article
- Development of CypriSSR: a genome-wide, chromosome-level microsatellite database for multiple cyprinidae species.Database : the journal of biological databases and curation · 2026Article
- Genomic Characterization and Phylogenetic Relationships ofAnimals : an open access journal from MDPI · 2026Article
- Article
- Microsatellite Markers Developed Based on Transcriptomic Data Reveal the Genetic Diversity and Population Genetic Structure ofBiology · 2025Article
- Pytrf: a python package for finding tandem repeats from genomic sequences.BMC bioinformatics · 2025Article
- Whole-Genome Sequencing ofAnimals : an open access journal from MDPI · 2025Article
- Parentage Verification and Segregation Distortion Patterns of Microsatellite Markers in Olive Flounder (Animals : an open access journal from MDPI · 2025Article
- Microsatellite repeat mapping shows inner chromosomal diversification in highly conserved karyotypes of Asian cyprinid fishes.Comparative cytogenetics · 2025Article
- Genome-Wide Microsatellites inAnimals : an open access journal from MDPI · 2024Article
- Genome-Wide In Silico Analysis of Microsatellite Loci in Rabbits.Animals : an open access journal from MDPI · 2024Article
- A Whole-Genome Survey and the Mitochondrial Genome ofAnimals : an open access journal from MDPI · 2024Article
- Comparison of the Distribution Patterns of Microsatellites Across the Genomes of Reptiles.Ecology and evolution · 2024Article
- Microsatellite density landscapes illustrate short tandem repeats aggregation in the complete reference human genome.BMC genomics · 2024Article
- Whole-Genome Survey Analyses of Five Goby Species Provide Insights into Their Genetic Evolution and Invasion-Related Genes.International journal of molecular sciences · 2024Article
- SSBlazer: a genome-wide nucleotide-resolution model for predicting single-strand break sites.Genome biology · 2024Article
- Characterization of 35 new microsatellite markers for the blacktip reef shark (Carcharhinus melanopterus) and cross-species amplification in eight other shark species.Molecular biology reports · 2023Article
- Microsatellite Analysis Revealed Potential DNA Markers for Gestation Length and Sub-Population Diversity in Kari Sheep.Animals : an open access journal from MDPI · 2022Article
- Whole-Genome Survey and Microsatellite Marker Detection of Antarctic Crocodile Icefish,Animals : an open access journal from MDPI · 2022Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMicrosatellite repeats are ubiquitous in organism genomes and play an important role in the chromatin organization, regulation of gene activity, recombination and DNA replication. Although microsatellite distribution patterns have been studied in most phylogenetic lineages, they are unclear in fish species.
resultsHere, we present the first systematic examination of microsatellite distribution in coding and non-coding regions of 14 fish genomes. Our study showed that the number and type of microsatellites displayed nonrandom distribution for both intragenic and intergenic regions, suggesting that they have potential roles in transcriptional or translational regulation and DNA replication slippage theories alone were insufficient to explain the distribution patterns. Our results showed that microsatellites are dominant in non-coding regions. The total number of microsatellites ranged from 78,378 to 1,012,084, and the relative density varied from 4925.76 bp/Mb to 25,401.97 bp/Mb. Overall, (A + T)-rich repeats were dominant. The dependence of repeat abundance on the length of the repeated unit (1-6 nt) showed a great similarity decrease, whereas more tri-nucleotide repeats were found in exonic regions than tetra-nucleotide repeats of most species. Moreover, the incidence of different repeated types appeared species- and genomic-specific. These results highlight potential mechanisms for maintaining microsatellite distribution, such as selective forces and mismatch repair systems.
conclusionsOur data could be beneficial for the studies of genome evolution and microsatellite DNA evolutionary dynamics, and facilitate the exploration of microsatellites structural, function, composition mode and molecular markers development in these species.
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