Alam Chaudhary Mashhood, Singh Avadhesh Kumar, Sharfuddin Choudhary, Ali Safdar
Department of Botany, Patna University, Bihar 800005, India.
Department of Biomedical Sciences, Shaheed Rajguru College of Applied Sciences for Women (SRCASW), University of Delhi, Vasundhara Enclave, New Delhi 110096, India.
Infect Genet Evol. 2014 Jan;21:287-94. doi: 10.1016/j.meegid.2013.11.018. Epub 2013 Nov 28.
An exhaustive compilation and analysis of incidence, distribution and variation of simple sequence repeats (SSRs) in viruses are required to understand the evolution and functional aspects of repetitive sequences. Present study focuses on the analysis of SSRs in 32 species of carlaviruses. The full length genome sequences were assessed from NCBI (http://www.ncbi.nlm.nih.-gov/) and analyzed using IMEx software. Variance in incidence of SSRs was observed, independent of genome size. Though the conversion of SSRs to imperfect microsatellite or compound SSR is low; compound microsatellites constituted by variant motifs accounted for up to 12.5% of the SSRs. Mononucleotide A/T is most prevalent followed by dinucleotide GT/TG and trinucleotide AAG/GAA in these genomes. The SSR and cSSR are predominantly localized to the coding region RDRP (RNA dependent RNA polymerase) and ORF-6 (open reading frame). The relative frequency of different classes of simple and compound microsatellites has been highlighted in accordance with the biology of carlavirus. Characterization of such variations would be pivotal for deciphering the enigma of these widely used, but incompletely understood sequences.
为了解重复序列的进化和功能方面，需要对病毒中简单序列重复（SSR）的发生率、分布和变异进行详尽的汇编和分析。本研究聚焦于对32种香石竹潜隐病毒属病毒的SSR分析。从NCBI（http://www.ncbi.nlm.nih.-gov/）获取全长基因组序列，并使用IMEx软件进行分析。观察到SSR发生率的差异，与基因组大小无关。虽然SSR转变为不完全微卫星或复合SSR的比例较低；由变异基序构成的复合微卫星占SSR的比例高达12.5%。在这些基因组中，单核苷酸A/T最为普遍，其次是二核苷酸GT/TG和三核苷酸AAG/GAA。SSR和复合SSR主要定位于编码区RNA依赖的RNA聚合酶（RDRP）和开放阅读框6（ORF-6）。根据香石竹潜隐病毒属病毒的生物学特性，突出显示了不同类型简单和复合微卫星的相对频率。此类变异的特征描述对于破解这些广泛使用但尚未完全理解的序列之谜至关重要。
