Incidence,complexity and diversity of simple sequence repeats across potexvirus genomes |
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Authors: | Chaudhary Mashhood Alam Avadhesh Kumar Singh Choudhary Sharfuddin Safdar Ali |
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Institution: | 1. Department of Botany, Patna University, Bihar 800005, India;2. Department of Biomedical Sciences, SRCASW, University of Delhi, Vasundhara Enclave, New Delhi 110096, India |
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Abstract: | An in-silico analysis of simple sequence repeats (SSRs) in genomes of 32 species of potexviruses was performed wherein a total of 691 SSRs and 33 cSSRs were observed. Though SSRs were present in all the studied genomes their incident frequency ranged from 11 to 30 per genome. Further, 10 potexvirus genomes possessed no cSSRs when extracted at a dMAX of 10 and wherein present, the highest frequency was 3. SSR and cSSR incidence, relative density and relative abundance were non-significantly correlated with genome size and GC content suggesting an ongoing evolutionary and adaptive phase of the virus species. SSRs present primarily ranged from mono- to tri-nucleotide repeat motifs with a greatly skewed distribution across the coding and non-coding regions. Present work is an effort for the undergoing compilation and analysis of incidence, distribution and variation of the viral repeat sequences to understand their evolutionary and functional relevance. |
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Keywords: | SSR simple sequence repeat cSSR compound simple sequence repeat IMEx Imperfect Microsatellite Extraction RD relative density RA relative abundance RDRP RNA dependent RNA polymerase TGB triple gene block CP coat protein |
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