Simple sequence repeats in mycobacterial genomes |
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Authors: | Vattipally B Sreenu Pankaj Kumar Javaregowda Nagaraju Hampapathalu A Nagarajaram |
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Institution: | (1) Laboratory of Computational Biology, Centre for DNA Fingerprinting and Diagnostics, ECIL Road, Nacharam, Hyderabad, 500 076, India;(2) Laboratory of Molecular Genetics, Centre for DNA Fingerprinting and Diagnostics, ECIL Road, Nacharam, Hyderabad, 500 076, India |
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Abstract: | Simple sequence repeats (SSRs) or microsatellites are the repetitive nucleotide sequences of motifs of length 1–6 bp. They
are scattered throughout the genomes of all the known organisms ranging from viruses to eukaryotes. Microsatellites undergo
mutations in the form of insertions and deletions (INDELS) of their repeat units with some bias towards insertions that lead
to microsatellite tract expansion. Although prokaryotic genomes derive some plasticity due to microsatellite mutations they
have in-built mechanisms to arrest undue expansions of microsatellites and one such mechanism is constituted by post-replicative
DNA repair enzymes MutL, MutH and MutS. The mycobacterial genomes lack these enzymes and as a null hypothesis one could expect
these genomes to harbour many long tracts. It is therefore interesting to analyse the mycobacterial genomes for distribution
and abundance of microsatellites tracts and to look for potentially polymorphic microsatellites. Available mycobacterial genomes,
Mycobacterium avium, M. leprae, M. bovis and the two strains of M. tuberculosis (CDC1551 and H37Rv) were analysed for frequencies and abundance of SSRs. Our analysis revealed that the SSRs are distributed
throughout the mycobacterial genomes at an average of 220–230 SSR tracts per kb. All the mycobacterial genomes contain few
regions that are conspicuously denser or poorer in microsatellites compared to their expected genome averages. The genomes
distinctly show scarcity of long microsatellites despite the absence of a post-replicative DNA repair system. Such severe
scarcity of long microsatellites could arise as a result of strong selection pressures operating against long and unstable
sequences although influence of GC-content and role of point mutations in arresting microsatellite expansions can not be ruled
out. Nonetheless, the long tracts occasionally found in coding as well as non-coding regions may account for limited genome
plasticity in these genomes.
Supplementary Data pertaining to this article is available on the Journal of Biosciences Website at |
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Keywords: | Comparative genomics genome analysis microsatellite mycocateria polymorphalism sequence repeats |
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