Abstract
Microsatellites, or simple sequence repeats (SSRs), contain repetitive DNA sequence where tandem repeats of one to six base pairs are present number of times. Chloroplast genome sequences have been shown to possess extensive variations in the length, number and distribution of SSRs. However, a comparative analysis of chloroplast microsatellites is not available. Considering their potential importance in generating genomic diversity, we have systematically analysed the abundance and distribution of simple and compound microsatellites in 164 sequenced chloroplast genomes from wide range of plants. The key findings of these studies are (1) a large number of mononucleotide repeats as compared to SSR2–6(di-, tri-, tetra-, penta-, hexanucleotide repeats) are present in all chloroplast genomes investigated, (2) lower plants such as algae show wide variation in relative abundance, density and distribution of microsatellite repeats as compared to flowering plants, (3) longer SSRs are excluded from coding regions of most chloroplast genomes, (4) GC content has a weak influence on number, relative abundance and relative density of mononucleotide as well as SSR2–6. However, GC content strongly showed negative correlation with relative density (R 2 = 0.5, P < 0.05) and relative abundance (R 2 = 0.6, P < 0.05) of cSSRs. In summary, our comparative studies of chloroplast genomes illustrate the variable distribution of microsatellites and revealed that chloroplast genome of smaller plants possesses relatively more genomic diversity compared to higher plants.
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Acknowledgments
We acknowledge Blessy software solution and The Science & Engineering Research Board, DST, Government of India for funding support. Authors are thankful to Dr. Girish K Srivastava, Actual: Prof. Colaborador Honorífico, IOBA, University of Valladolid, Spain and Dr. Umesh C.S. Yadav, SLS, CUG for language editing.
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The authors declare that they have no competing interests.
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Communicated by M. Kupiec.
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George, B., Bhatt, B.S., Awasthi, M. et al. Comparative analysis of microsatellites in chloroplast genomes of lower and higher plants. Curr Genet 61, 665–677 (2015). https://doi.org/10.1007/s00294-015-0495-9
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DOI: https://doi.org/10.1007/s00294-015-0495-9