Abstract
Microsatellites are short tandem DNA repeats, ubiquitous in genomes. They are believed to be under selection pressure, considering their high distribution and abundance beyond chance or random accumulation. However, limited analysis of microsatellites in single taxonomic groups makes it challenging to understand their evolutionary significance across taxonomic boundaries. Despite abundant genomic information, microsatellites have been studied in limited contexts and within a few species, warranting an unbiased examination of their genome-wide distribution in distinct versus closely related-clades. Large-scale comparisons have revealed relevant trends, especially in vertebrates. Here, “MicrosatNavigator”, a new tool that allows quick and reliable investigation of perfect microsatellites in DNA sequences, was developed. This tool can identify microsatellites across the entire genome sequences. Using this tool, microsatellite repeat motifs were identified in the genome sequences of 186 vertebrates. A significant positive correlation was noted between the abundance, density, length, and GC bias of microsatellites and specific lineages. The (AC)n motif is the most prevalent in vertebrate genomes, showing distinct patterns in closely related species. Longer microsatellites were observed on sex chromosomes in birds and mammals but not on autosomes. Microsatellites on sex chromosomes of non-fish vertebrates have the lowest GC content, whereas high-GC microsatellites (≥ 50 M% GC) are preferred in bony and cartilaginous fishes. Thus, similar selective forces and mutational processes may constrain GC-rich microsatellites to different clades. These findings should facilitate investigations into the roles of microsatellites in sex chromosome differentiation and provide candidate microsatellites for functional analysis across the vertebrate evolutionary spectrum.
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Data availability
The full dataset and metadata from this publication are available from the Dryad Digital Repository. Dataset, https://datadryad.org/stash/share/S15Z3AqzS8sXqrlUzi9ts2w_RezgFklBJCXRHcs0u2o (accessed on 13 April 2023).
Abbreviations
- ANOVA:
-
Analysis of variance
- Bkm:
-
Banded krait minor-satellite repeats
- chrRD:
-
Chromosome-wide relative density
- CS:
-
Cuckoo-search
- DE:
-
Differential evolution
- EMD:
-
Exact microsatellite discovery
- ENA:
-
European Nucleotide Archive
- FISH:
-
Fluorescence in situ hybridization
- GA:
-
Genetic algorithm
- GC:
-
Guanine-cytosine
- gcRA:
-
GC content category of relative abundance
- gRD:
-
Genome-wide relative density
- NCBI:
-
National Center for Biotechnology Information
- NGS:
-
Next-generation sequencing
- PMP:
-
Panted (l, d) motif problem
- PSWM:
-
Position-specific weight matrix
- RA:
-
Relative abundance
- RDfd:
-
Fold-difference in relative density
- rDNA:
-
Ribosomal DNA
- SSR:
-
Simple sequence repeat
- TE:
-
Transposable elements
- TFBS:
-
Transcription factor binding site
- TSV:
-
Tab-separated values
- WGS:
-
Whole-genome sequencing
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Acknowledgements
The authors extend grateful thanks to the Center for Agricultural Biotechnology, Kasetsart University, Nakhon Pathom, Thailand, and NSTDA Supercomputer Center (ThaiSC), Pathum Thani, Thailand, for providing computational infrastructures. We also gratefully acknowledge the Center for Bio-Medical Engineering Core Facility at Dankook University, Cheonan, South Korea. We also thank the Faculty of Science for providing supporting research facilities. We express our gratitude to Sucha Supittayapornpong (Vidyasirimedhi Institute of Science and Technology, Thailand) for valuable discussions.
Funding
This research was financially supported by a grant from the Faculty of Science, Kasetsart University, Thailand (No.6501.0901.1/574) awarded to R.R. and K.S.; the High-Quality Research Graduate Development Cooperation Project between Kasetsart University and the National Science and Technology Development Agency (NSTDA) awarded to T.P. and K.S.; the Thailand Science Research and Innovation through the Kasetsart University Reinventing University Program 2021 (3/2564) awarded to T.P., A.L. and K.S.; the e-ASIA Joint Research Program (no. P1851131) awarded to W.S. and K.S.; the National Science and Technology Development Agency (NSTDA) (NSTDA P-19–52238 and JRA-CO-2564–14003-TH) awarded to W.S. and K.S.; the National Research Council of Thailand (NRCT/2565) awarded to K.S.; the National Research Council of Thailand, National Science and Technology Development Agency (NSTDA), and Thailand Science Research and Innovation (TSRI) (N42A660605) awarded to W.S., S.F.A., E.K., P.D., N.M., and K.S.; the Kasetsart University Research and Development Institute (FF (KU)25.64 and FF(S-KU)17.66) and a support from the International SciKU Branding (ISB), Faculty of Science, Kasetsart University awarded to W.S., S.F.A., and K.S.
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Conceptualization, K.S; methodology R.R., P.W., S.F.A., and K.S.; software, R.R., P.W., and S.F.A.; formal analysis, R.R. and K.S.; writing—original draft preparation, R.R. and K.S.; writing—review and editing, R.R., P.W., T.P., K.J., A.L., T.T., W.S., S.F.A., K.H., E.K., N.M., A.K., P.D., A.A. and K. S.; visualization, R.R., P.W., T.P., W.S., and K.S.; project administration, K.S.; funding acquisition, K.S. All authors have read and agreed to the published version of the manuscript.
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Rasoarahona, R., Wattanadilokchatkun, P., Panthum, T. et al. MicrosatNavigator: exploring nonrandom distribution and lineage-specificity of microsatellite repeat motifs on vertebrate sex chromosomes across 186 whole genomes. Chromosome Res 31, 29 (2023). https://doi.org/10.1007/s10577-023-09738-4
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DOI: https://doi.org/10.1007/s10577-023-09738-4