有尾噬菌体目中微卫星和复合型微卫星的发生及分析

doi:10.13523/j.cb.20141104

中国生物工程杂志

2014, Vol. 34

Issue (11): 24-33 DOI: 10.13523/j.cb.20141104

计算生物学与生物信息学专辑

有尾噬菌体目中微卫星和复合型微卫星的发生及分析

周兰¹, 吴晓龙¹, 付永卓¹, 赵相艳¹, 陈禹保², 谭钟扬¹

1. 湖南大学生物学院生物信息学长沙 410082;
2. 北京市科学技术研究院北京市计算中心北京 100094

Occurrence and Analysis of Microsatellites and Compound Microsatellites in Caudovirales

ZHOU Lan¹, WU Xiao-long¹, FU Yong-zhuo¹, ZHAO Xiang-yan¹, CHEN Yu-bao², TAN Zhong-yang¹

1. College of Biology, Hunan University, Changsha 410082, China;
2. Department of Computational Biology, Beijing Computing Center, Yongfeng Industry Base, Beijing 100094, China

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摘要：

简单重复序列亦称微卫星,被成功应用于许多真核生物、原核生物和病毒的基因组和进化研究,但是噬菌体中的微卫星目前很少被研究。因此对60条尾病毒目基因组中的微卫星和和复合型微卫星(由两个或两个以上直接相邻的微卫星组成)做综合性分析,在这60个基因组中总共观察到11 874个微卫星和449个复合型微卫星。相关性分析表明微卫星个数与基因组大小成正线性相关(ρ=0.899, P<0.01)。参考序列中的微卫星个数少于对应的随机序列中微卫星个数,这种反常现象主要是因为参考序列含有较少的单核苷酸和二核苷酸重复。A/T和AT/TA重复是单核苷酸和二核苷酸重复中最主要的类型,因此单核苷酸重复中的GC含量明显低于相应的序列中的GC含量;相比之下,微卫星中的二核苷酸和三核苷酸重复的GC含量与对应的参考序列的GC含量无明显区别。尾病毒目基因组中的这些结果与其它生物体基因组存在一定的差别。有助于了解尾病毒目中微卫星的分布、进化和生物学功能。

关键词： 微卫星复合型; 微卫星噬菌体; 尾病毒目; 分布

Abstract:

Simple sequence repeats (SSRs) or microsatellites have been successfully used for various genetic and evolutionary studies in eukaryotic, prokaryotic and viral systems, but information regarding SSRs in bacteriophages is limited by lack of studies. We made a comprehensive analysis of microsatellites and compound microsatellites (composed of two or more microsatellites residing directly adjacent to each other) in 60 Caudovirales genomes, and a total of 11 874 microsatellites and 449 compound microsatellites were observed in these genomes. In general, the count of SSRs is proportional to genome size by Pearson linear correlation analysis (ρ=0.899,P<0.01). Microsatellites in reference sequences are lower than that in random sequences, and it was beyond our expectation. The primarily reason was that reference sequences contain fewer mononucleotide and dinucleotide repeats. A/T and AT/TA were predominant in mononucleotide and dinucleotide repeats in most sequences, so GC content in mononucleotide repeats was notably lower than that in corresponding genome; by contrast, GC content has no significant difference between reference sequences and microsatellites of dinucletide and trinucleotide repeats. These results in Caudovirales are more or less different from other organisms' genomes. Our study might be helpful in understanding the distribution, evolution and biological function of microsatellites in Caudovirales.

Key words: Microsatellite Compound microsatellite Bacteriophage Caudovirales Distribution

收稿日期: 2014-09-20 出版日期: 2014-11-25

ZTFLH:

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通讯作者: 谭钟扬,zhongyang@hnu.edu.cn E-mail: zhongyang@hnu.edu.cn

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引用本文:

周兰, 吴晓龙, 付永卓, 赵相艳, 陈禹保, 谭钟扬. 有尾噬菌体目中微卫星和复合型微卫星的发生及分析[J]. 中国生物工程杂志, 2014, 34(11): 24-33.

ZHOU Lan, WU Xiao-long, FU Yong-zhuo, ZHAO Xiang-yan, CHEN Yu-bao, TAN Zhong-yang. Occurrence and Analysis of Microsatellites and Compound Microsatellites in Caudovirales. China Biotechnology, 2014, 34(11): 24-33.

链接本文:

https://manu60.magtech.com.cn/biotech/CN/10.13523/j.cb.20141104 或 https://manu60.magtech.com.cn/biotech/CN/Y2014/V34/I11/24

[1] Ellegren H. Microsatellites: simple sequences with complex evolution. Nat Rev Genet, 2004, 5: 435-445.

[2] Rajendrakumar P, Biswal A K, Balachandran S M, et al. Simple sequence repeats in organellar genomes of rice: frequency and distribution in genic and intergenic regions. Bioinformatics, 2007, 23: 1-4.

[3] Toth G, Gaspari Z, Jurka J. Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res, 2000, 10(7): 967-981.

[4] Gur-Arie R, Cohen C J. Simple sequence repeats in Escherichia coli: abundance, distribution, composition, and polymorphism. Genome Res, 2000, 10(1): 62-71.

[5] Chen M, Tan Z, Zeng G. Microsatellite is an important component of complete Hepatitis C virus genomes. Infect Genet Evol, 2011a, 11(7): 1646-1654.

[6] Ouyang Q, Zhao X, Feng H, et al. High GC content of simple sequence repeats in Herpes simplex virus type 1 genome. Gene, 2012, 499(1): 37-40.

[7] Chen M, Tan Z, Zeng G, et al. Differential distribution of compound microsatellites in various Human Immunodeficiency Virus Type 1 complete genomes. Infect Genet Evol, 2012, 12(7):1452-1457.

[8] Kofler R, Schlotterer C, Luschutzky E, et al. Survey of microsatellite clustering in eight fully sequenced species sheds light on the origin of compound microsatellites. BMC Genomics, 2008, 9: 612.

[9] Pinto L R, Oliveira K M, Marconi T, et al. Characterization of novel sugarcane expressed sequence tag microsatellites and their comparison with genomic SSRs. Plant Breeding, 2006, 125(4): 378-384.

[10] McCouch S R, Teytelman L, Xu Y, et al. Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res, 2002, 9(6):257-279.

[11] Somers D J, Isaac P, Edwards K. A high-density microsatellite consensus map for bread wheat (Triticum aestivum L.). Theor Appl Genet, 2004, 109(6):1105-1114.

[12] Innan H, Terauchi R, Miyashita N T. Microsatellite polymorphism in natural populations of the wild plant Arabidopsis thaliana. Genetics, 1997, 146(4):1441-1452.

[13] Bowers J E, Meredith C P. The parentage of a classic wine grape, Cabernet Sauvignon. Nat Genet, 1997, 16(1):84-87.

[14] Garza J C, Slatkin M, Freimer N B. Microsatellite allele frequencies in humans and chimpanzees, with implications for constraints on allele size. Mol Biol Evol, 1995, 12(4):594-603.

[15] MacHugh D E, Shriver M D, Loftus R T, et al. Microsatellite DNA variation and the evolution, domestication and phylogeography of taurine and Zebu cattle (Bos taurus and Bos indicus). Genetics, 1997, 146(3):1071-1086.

[16] Bates G, Lehrach H. Trinucleotide repeat expansions and human genetic disease. BioEssays, 1994, 16(4):277-284.

[17] Wooster R, Cleton-Jansen A M, Collins N, et al. Instability of short tandem repeats (microsatellites) in human cancer. Nat Genet, 1994, 6:152-156.

[18] Fokine A, Rossmann M G. Molecular architecture of tailed doublestranded DNA phages. Bacteriophage, 2014, 4(1):e28281.

[19] Wommack K E, Colwell R R. Virioplankton: Viruses in aquatic ecosystems. Microbiol Mol Biol Rev, 2000, 64(1): 69-114.

[20] Hendrix R W. Bacteriophages: Evolution of the Majority. Theoretical Population Biology, 2002, 61(4): 471-480.

[21] King A M Q, Adams M J, Carstens E B, et al. Virus taxonomy: Ninth Report of the International Committee on Taxonomy of Viruses. San Diego: Academic Press, 2012, 39-85.

[22] Mudunuri S B, Nagarajaram H A. IMEx: imperfect microsatellite extractor. Bioinformatics, 2007, 23(10): 1181-1187.

[23] Alam C M, George B, Sharfuddin C, et al. Occurrence and analysis of imperfect microsatellites in diverse potyvirus genomes. Gene, 2013a, 521(2): 238-244.

[24] Alam C M, Singh A K, Sharfuddin C, et al. In-silico analysis of simple and imperfect microsatellites in diverse tobamovirus genomes. Gene,2013b, 530(2): 193-200.

[25] Singh A K, Alam C M, Sharfuddin C, et al. Frequency and distribution of simple and compound microsatellites in forty-eight Human papillomavirus (HPV) genomes. Infect Genet Evol, 2014, 24: 92-98.

[26] Alam C M, Singh A K, Sharfuddin C, et al. Genome-wide scan for analysis of simple and imperfect microsatellites in diverse carlaviruses. Infect Genet Evol, 2014a, 21: 287-294.

[27] Chen M, Zeng G, Tan Z, et al. Compound microsatellites in complete Escherichia coli genomes. FEBS Lett, 2011b, 585(7): 1072-1076.

[28] Chen M, Tan Z, Jiang J, et al. Similar distribution of simple sequence repeats in diverse completed human immunodeficiency virus type 1 genomes. FEBS Lett, 2009, 583(17): 2959-2963.

[29] Alam C M, Singh A K, Sharfuddin C, et al. Incidence, complexity and diversity of simple sequence repeats across potexvirus genomes. Gene, 2014b, 537(2): 189-196.

[30] Wu X, Zhou L, Zhao X, et al. The analysis of microsatellites and compound microsatellites in 56 complete genomes of Herpesvirales. Gene, 2014, 551: 103-109.

[31] Kashi Y, King D G. Simple sequence repeats as advantageous mutators in evolution. Trends Genet, 2006, 22 (5): 253-259.

[32] Zhao X, Tian Y, Yang R, et al. Coevolution between simple sequence repeats (SSRs) and virus genome size. BMC Genomics, 2012, 13: 435.

[33] Hancock J M. Genome size and the accumulation of simple sequence repeats: implications of new data from genome sequencing projects. Genetica, 2002, 115(1): 93-103.

[34] Karaoglu H, Lee C M, Meyer W. Survey of simple sequence repeats in completed fungal genomes. Mol Biol Evol, 2005, 22(3): 639-649.

[35] Qin L, Zhang Z, Zhao X, et al. Survey and analysis of simple sequence repeats (SSRs) present in the genomes of plant viroids. FEBS Open Bio, 2014, 4:185-189.

[36] Jurka J, Pethiyagoda C. Simple repetitive DNA sequences from primates: compilation and analysis. J Mol Evol, 1995, 40(2):120-126.

[37] Katti M V, Ranjekar PK, Guota V S. Differential distribution of simple sequence repeats in eukaryotic genomes. Mol Biol Evol, 2001, 18(7): 1161-1167.

[38] Hummerich H, Lehrach H. Trinucleotide repeat expansion and human disease. Electrophoresis, 1995, 16(1): 1698-1704.

[39] Hiratani I, Leskovar A, Gilbert D M. Differentiation-induced replication-timing changes are restricted to AT-rich/long interspersed nuclear element (LINE)-richisochores. Proc Natl Acad Sci U S A, 2004, 101(48): 16861-16866.

[40] Ren L, Gao G, Zhao D, et al. Developmental stage related patterns of codon usage and genomic GC content: searching for evolutionary fingerprint by models of stem cell differentiation. Genome Biol, 2007, 8(3): R35.

[41] Vinogradov A E. Bendable genes of warm-blooded vertebrates. Mol Biol Evol, 2001, 18(12): 2195-2200.

[42] Vinogradov A E. DNA helix: the importance of being GC-rich. Nucleic Acids Res, 2003, 31(7): 1838-1844.

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