George B, Mashhood Alam Ch, Jain S K, Sharfuddin Ch, Chakraborty S
Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
Virus Genes. 2012 Dec;45(3):556-66. doi: 10.1007/s11262-012-0802-1. Epub 2012 Aug 18.
Microsatellites are tandem repeat sequences with repeat unit of one to six base pairs. Although, microsatellites have been studied in eukaryotes as well as prokaryotes, information on their occurrence on virus genomes is limited. We examined microsatellite distribution in 263 complete geminivirus genomes. Results indicated microsatellites to be an important component of geminiviral genomes. For each geminiviral genome, mono- and dinucleotide repeats were found to be highly predominant. Occurrence of microsatellites within geminiviral genome is significantly lesser than organisms with higher genome sizes and their number decreased with an increase in the length of repeat unit. Repeats of AT/TA, GT/TG, CT/TC, CTT/TTC, and GAA/AAG occurred with high frequency, whereas CG/GC, CGA/AGC, AAC/CAA, and GCT/TCG repeats had rare incidence. Interesting observation related to differential distribution of simple sequence repeats in genomic components of begomoviruses has been noted. We discussed the possible reasons for the observed divergence. To our knowledge, this is the first analysis of microsatellites occurring in any ssDNA viral genome for such purposes and represents a general approach for analysis of other viral genomes. The presence of microsatellites in geminiviral genomes may be used to obtain information regarding viral genetic diversity, evolution, and strain (isolate) identification.
微卫星是由1至6个碱基对的重复单元组成的串联重复序列。尽管微卫星已在真核生物和原核生物中得到研究，但关于它们在病毒基因组中的存在情况的信息有限。我们研究了263个完整双生病毒基因组中的微卫星分布。结果表明微卫星是双生病毒基因组的重要组成部分。对于每个双生病毒基因组，单核苷酸和二核苷酸重复序列被发现高度占主导地位。双生病毒基因组中微卫星的出现频率明显低于基因组较大的生物体，并且其数量随着重复单元长度的增加而减少。AT/TA、GT/TG、CT/TC、CTT/TTC和GAA/AAG的重复序列出现频率较高，而CG/GC、CGA/AGC、AAC/CAA和GCT/TCG重复序列的发生率较低。已经注意到与双生病毒基因组成分中简单序列重复的差异分布相关的有趣观察结果。我们讨论了观察到的差异的可能原因。据我们所知，这是首次出于此类目的对任何单链DNA病毒基因组中出现的微卫星进行分析，并且代表了分析其他病毒基因组的一般方法。双生病毒基因组中微卫星的存在可用于获取有关病毒遗传多样性、进化和毒株（分离株）鉴定的信息。
