Occurrence and analysis of imperfect microsatellites in diverse potyvirus genomes |
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Authors: | Ch. Mashhood Alam B. George Ch. Sharfuddin S.K. Jain S. Chakraborty |
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Affiliation: | 1. Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India;2. Department of Botany, Patna University, Patna, Bihar, India;3. Department of Biotechnology, Jamia Hamdard University, New Delhi, India |
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Abstract: | Simple sequence repeats (SSRs) or microsatellites are known to exhibit ubiquitous across all kingdoms of life including viruses. However, imperfections in simple sequence repeats have been analyzed in genomes of human, Escherichia coli and Human Immunodeficiency virus. The assessment of compound microsatellites in plant viral genomes is yet to be studied. Potyviruses severely affect crop plant growth and reduce economic yield in diverse cropping systems worldwide. Hence, we analyze the nature and distribution of compound microsatellites present in complete genome of 45 potyvirus species. The results indicate that compound microsatellites accounted for about 0% to 15.15% of all microsatellites and have low complexity as compared to that of prokaryotic genomes. Overall, 14% of compound microsatellites were of similar motifs and such motif duplications were observed for CA, TA and AG repeats. Among all 45 potyvirus genomes analyzed, SSR couple (AG)-x-(AC) was found to be the most abundant one. Hence it is apparent that in contrast to eukaryotes, majority of compound microsatellites in potyviruses were composed of variant motifs. We also highlight the relative frequency of different classes of compound microsatellites as well as their patterns of distribution and correlate with biology of potyviruses. Further characterization of such variation is important for elucidating the origin, mutational processes, and structure of these widely used, but incompletely understood sequences. |
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Keywords: | SSR, Simple sequence repeat cSSR, Compound simple sequence repeat IMEx, Imperfect Microsatellite Extraction dMAX, Maximum distance allowed between two simple sequence repeat RD, Relative density RA, Relative abundance HC-Pro, Helper component proteinase CP, Coat protein RDRP, RNA dependent RNA polymerase CDFD, Centre for DNA Fingerprinting and Diagnostics |
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