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.
Highlights
Microsatellite repeats are ubiquitous in organism genomes and play an important role in the chromatin organization, regulation of gene activity, recombination and DNA replication
Microsatellite repeats are advantageous as genetic markers due to their high polymorphism, informativeness and co-dominance, and have been used to construct quantitative trait loci (QTL) maps, genetic linkage maps [14,15,16,17,18] and DNA fingerprinting [19]
Distribution patterns of microsatellite repeats in the fish genomes We examined the number, relative frequency, relative density, GC content and the coverage degree of microsatellites with motif lengths of 1–6 nucleotides in the 14 fish genomes (Table 2)
Summary
Microsatellite repeats are ubiquitous in organism genomes and play an important role in the chromatin organization, regulation of gene activity, recombination and DNA replication. Microsatellite repeats are advantageous as genetic markers due to their high polymorphism, informativeness and co-dominance, and have been used to construct quantitative trait loci (QTL) maps, genetic linkage maps [14,15,16,17,18] and DNA fingerprinting [19]. These features provide the foundation for their successful application in other fundamental and applied fields of biology, including population and conservation genetics, genetic dissection of complex traits and marker-assisted breeding programs [10, 20,21,22]
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