Microsatellite is an important component of complete Hepatitis C virus genomes

Infection, Genetics and Evolution

Volumn 11, Issue 7, 2011, Pages 1646-1654

  Chen, Ming ^a   Tan, Zhongyang ^a   Zeng, Guangming ^a  

^a HUNAN UNIVERSITY   (China)

Author keywords

Comparative genomics; Hepatitis C virus; Microsatellite; Simple sequence repeat

Indexed keywords

MICROSATELLITE DNA;

ARTICLE; CONTROLLED STUDY; DINUCLEOTIDE REPEAT; EUKARYOTE; GENOME SIZE; GENOTYPE; HEPATITIS C VIRUS; NONHUMAN; NUCLEOTIDE REPEAT; NUCLEOTIDE SEQUENCE; POPULATION GENETICS; PRIORITY JOURNAL; PROKARYOTE; STRAIN IDENTIFICATION; TRINUCLEOTIDE REPEAT; VIRUS GENOME;

DINUCLEOTIDE REPEATS; DNA, VIRAL; GENOME, VIRAL; HEPACIVIRUS; HUMANS; MICROSATELLITE INSTABILITY; MICROSATELLITE REPEATS;

EUKARYOTA; HEPATITIS C VIRUS; PROKARYOTA;

EID: 80053573321     PISSN: 15671348     EISSN: 15677257     Source Type: Journal    
DOI: 10.1016/j.meegid.2011.06.012     Document Type: Article

References (39)

1. Ackermann M., Chao L. DNA sequences shaped by selection for stability. PLoS Genet. 2006, 2:e22.
2. Chen M., Tan Z., Jiang J., Li M., Chen H., Shen G., Yu R. Similar distribution of simple sequence repeats in diverse completed Human Immunodeficiency Virus Type 1 genomes. FEBS Lett. 2009, 583:2959-2963.
3. Chen M., Tan Z., Zeng G. MfSAT: detect simple sequence repeats in viral genomes. Bioinformation 2011, 6:171-172.
4. Chen M., Tan Z., Zeng G., Peng J. Comprehensive analysis of simple sequence repeats in pre-miRNAs. Mol. Biol. Evol. 2010, 27:2227-2232.
5. Chen M., Zeng G., Tan Z., Jiang M., Zhang J., Zhang C., Lu L., Lin Y., Peng J. Compound microsatellites in complete Escherichia coli genomes. FEBS Lett. 2011, 10.1016/j.febslet.2011.03.005.
6. Coenye T., Vandamme P. Characterization of mononucleotide repeats in sequenced prokaryotic genomes. DNA Res. 2005, 12:221-233.
7. Davis C.L., Field D., Metzgar D., Saiz R., Morin P.A., Smith I.L., Spector S.A., Wills C. Numerous length polymorphisms at short tandem repeats in human cytomegalovirus. J. Virol. 1999, 73:6265-6270.
8. de wachter R. The number of repeats expected in random nucleic acid sequences and found in genes. J. Theor. Biol. 1981, 91:71-98.
9. Deback C., Boutolleau D., Depienne C., Luyt C.E., Bonnafous P., Gautheret-Dejean A., Garrigue I., Agut H. Utilization of microsatellite polymorphism for differentiating herpes simplex virus type 1 strains. J. Clin. Microbiol. 2009, 47:533-540.
10. Dieringer D., Schlotterer C. Two distinct modes of microsatellite mutation processes: evidence from the complete genomic sequences of nine species. Genome Res. 2003, 13:2242-2251.
11. Ellegren H. Microsatellites: simple sequences with complex evolution. Nat. Rev. Genet. 2004, 5:435-445.
12. Gur-Arie R., Cohen C.J., Eitan Y., Shelef L., Hallerman E.M., Kashi Y. Simple sequence repeats in Escherichia coli: abundance, distribution, composition, and polymorphism. Genome Res. 2000, 10:62-71.
13. Hancock J.M. Genome size and the accumulation of simple sequence repeats: implications of new data from genome sequencing projects. Genetica 2002, 115:93-103.
14. Harr B., Schlotterer C. Long microsatellite alleles in Drosophila melanogaster have a downward mutation bias and short persistence times, which cause their genome-wide underrepresentation. Genetics 2000, 155:1213-1220.
15. Houng H.S., Lott L., Gong H., Kuschner R.A., Lynch J.A., Metzgar D. Adenovirus microsatellite reveals dynamics of transmission during a recent epidemic of human adenovirus serotype 14 infection. J. Clin. Microbiol. 2009, 47:2243-2248.
16. Karaoglu H., Lee C.M., Meyer W. Survey of simple sequence repeats in completed fungal genomes. Mol. Biol. Evol. 2005, 22:639-649.
17. Katti M.V., Ranjekar P.K., Gupta V.S. Differential distribution of simple sequence repeats in eukaryotic genome sequences. Mol. Biol. Evol. 2001, 18:1161-1167.
18. Kelkar Y.D., Tyekucheva S., Chiaromonte F., Makova K.D. The genome-wide determinants of human and chimpanzee microsatellite evolution. Genome Res. 2008, 18:30-38.
19. Kuiken C., Yusim K., Boykin L., Richardson R. The Los Alamos hepatitis C sequence database. Bioinformatics 2005, 21:379-384.
20. Kumar P., Chaitanya P.S., Nagarajaram H.A. PSSRdb: a relational database of polymorphic simple sequence repeats extracted from prokaryotic genomes. Nucleic Acids Res. 2011, 39:D601-D605.
21. Levinson G., Gutman G.A. Slipped-strand mispairing: a major mechanism for DNA sequence evolution. Mol. Biol. Evol. 1987, 4:203-221.
22. Li Y.C., Korol A.B., Fahima T., Nevo E. Microsatellites within genes: structure, function, and evolution. Mol. Biol. Evol. 2004, 21:991-1007.
23. Molla M., Delcher A., Sunyaev S., Cantor C., Kasif S. Triplet repeat length bias and variation in the human transcriptome. Proc. Natl. Acad. Sci. USA 2009, 106:17095-17100.
24. Mrazek J. Analysis of distribution indicates diverse functions of simple sequence repeats in Mycoplasma genomes. Mol. Biol. Evol. 2006, 23:1370-1385.
25. Mrazek J., Guo X., Shah A. Simple sequence repeats in prokaryotic genomes. Proc. Natl. Acad. Sci. USA 2007, 104:8472-8477.
26. Mudunuri S.B., Nagarajaram H.A. IMEx: imperfect microsatellite extractor. Bioinformatics 2007, 23:1181-1187.
27. Mudunuri S.B., Rao A.A., Pal lamsetty S., Mishra P., Nagarajaram H.A. VMD: viral microsatellite database - a comprehensive resource for all viral microsatellites. J. Comput. Sci. Syst. Biol. 2009, 2:283-286.
28. O'Dushlaine C.T., Edwards R.J., Park S.D., Shields D.C. Tandem repeat copy-number variation in protein-coding regions of human genes. Genome Biol. 2005, 6:R69.
29. Pearson C.E., Nichol Edamura K., Cleary J.D. Repeat instability: mechanisms of dynamic mutations. Nat. Rev. Genet. 2005, 6:729-742.
30. Power P.M., Sweetman W.A., Gallacher N.J., Woodhall M.R., Kumar G.A., Moxon E.R., Hood D.W. Simple sequence repeats in Haemophilus influenzae. Infect. Genet. Evol. 2009, 9:216-228.
31. Rajendrakumar P., Biswal A.K., Balachandran S.M., Srinivasarao K., Sundaram R.M. Simple sequence repeats in organellar genomes of rice: frequency and distribution in genic and intergenic regions. Bioinformatics 2007, 23:1-4.
32. Segarra A., Pepin J.F., Arzul I., Morga B., Faury N., Renault T. Detection and description of a particular Ostreid herpesvirus 1 genotype associated with massive mortality outbreaks of Pacific oysters, Crassostrea gigas, in France in 2008. Virus Res. 2010, 153:92-99.
33. Simmonds P. Genetic diversity and evolution of hepatitis C virus - 15 years on. J. Gen. Virol. 2004, 85:3173-3188.
34. n repetitive sequences in mammalian genomes. Genomics 1991, 10:807-815.
35. Tautz D., Trick M., Dover G.A. Cryptic simplicity in DNA is a major source of genetic variation. Nature 1986, 322:652-656.
36. Temnykh S., DeClerck G., Lukashova A., Lipovich L., Cartinhour S., McCouch S. Computational and experimental analysis of microsatellites in rice (Oryza sativa L.): frequency, length variation, transposon associations, and genetic marker potential. Genome Res. 2001, 11:1441-1452.
37. Toth G., Gaspari Z., Jurka J. Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res. 2000, 10:967-981.
38. Usdin K. The biological effects of simple tandem repeats: lessons from the repeat expansion diseases. Genome Res. 2008, 18:1011-1019.
39. Wierdl M., Dominska M., Petes T.D. Microsatellite instability in yeast: dependence on the length of the microsatellite. Genetics 1997, 146:769-779.