Genome wide survey of microsatellites in ssDNA viruses infecting vertebrates

Gene

Volumn 552, Issue 2, 2014, Pages 209-218

  Jain, Ankit ^a   Mittal, Nikhil ^a   Sharma, Prakash C ^a  

^a GURU GOBIND SINGH INDRAPRASTHA UNIVERSITY   (India)

Author keywords

DTTPH repeats; GC content; Genome size; Microsatellite distribution; Mononucleotide repeats; SsDNA virus

Indexed keywords

MICROSATELLITE DNA; SINGLE STRANDED DNA;

ANELLOVIRIDAE; ARTICLE; CIRCOVIRIDAE; DINUCLEOTIDE REPEAT; DNA BASE COMPOSITION; DNA VIRUS; DNA VIRUS INFECTION; GENOME ANALYSIS; GENOME SIZE; NONHUMAN; PARVOVIRUS; RELATIVE DENSITY; SIMPLE SEQUENCE REPEAT; TRINUCLEOTIDE REPEAT; VERTEBRATE; VIRUS ETIOLOGY; VIRUS GENOME; VIRUS PATHOGENESIS; GENETICS; PARVOVIRIDAE;

SSDNA VIRUSES; VERTEBRATA;

ANELLOVIRUS; CIRCOVIRIDAE; DNA, SINGLE-STRANDED; GENOME SIZE; GENOME, VIRAL; MICROSATELLITE REPEATS; PARVOVIRIDAE;

EID: 84908027040     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2014.09.032     Document Type: Article

References (43)

1. Alam C.M., Singh A.K., Sharfuddin C., Ali S. Wide scan for analysis of simple and imperfect microsatellites in diverse carlaviruses. Infect. Genet. Evol. 2013, 21:287-294.
2. Alam C.M., Singh A.K., Sharfuddin C., Ali S. Incidence, complexity and diversity of simple sequence repeats across potexvirus genomes. Gene 2014, 537:189-196.
3. Angly F.E., Felts B., Breitbart M., Salamon P., Edwards R.A., Carlson C., Chan A.M., Haynes M., Kelley S., Liu H., Mahaffy J.M., Mueller J.E., Nulton J., Olson R., Parsons R., Rayhawk S., Suttle C.A., Rohwer F. The marine viromes of four oceanic regions. PLoS Biol. 2006, 4:e368.
4. Belyi V.A., Levine A.J., Skalka A.M. Sequences from ancestral single-stranded DNA viruses in vertebrate genomes: the Parvoviridae and Circoviridae are more than 40 to 50millionyears old. J. Virol. 2010, 84:12458-12462.
5. Berns K., Parrish C.R. Parvoviridae. Fields Virology 2007, 2437-2478. Lippincott Williams & Wilkins, Philadelphia, PA. D.M. Knipe, P.M. Howley (Eds.).
6. Breitbart M., Salamon P., Andresen B., Mahaffy J.M., Segall A.M., Mead D., Azam F., Rohwer F. Genomic analysis of uncultured marine viral communities. Proc. Natl. Acad. Sci. U. S. A. 2002, 99:14250-14255.
7. 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.
8. Chen M., Tan Z., Zeng G. Microsatellite is an important component of complete hepatitis C virus genomes. Infect. Genet. Evol. 2011, 11:1646-1654.
9. Chen M., Tan Z., Zeng G., Zeng Z. Differential distribution of compound microsatellites in various human immunodeficiency virus type 1 complete genomes. Infect. Genet. Evol. 2012, 12:1452-1457.
10. Duffy S., Shackelton L.A., Holmes E.C. Review rates of evolutionary change in viruses: patterns and determinants. Nat. Rev. Genet. 2008, 9:267-276.
11. Ellegren H. Microsatellites: simple sequences with complex evolution. Nat. Rev. Genet. 2004, 5:435-445.
12. George B., Alam C.M., Jain S.K., Sharfuddin C., Chakraborty S. Differential distribution and occurrence of simple sequence repeats in diverse geminivirus genomes. Virus Genes 2012, 45:556-566.
13. Grover A., Sharma P.C. Is spatial occurrence of microsatellites in the genome a determinant of their function and dynamics contributing to genome evolution?. Curr. Sci. 2011, 100:859-869.
14. 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.
15. Jain A., Chaudhary S., Sharma P.C. Mining of microsatellites using next generation sequencing of seabuckthorn (Hippophae rhamnoides L.) transcriptome. Physiol. Mol. Biol. Plants 2014, 20:115-123.
16. Kashi Y., King D.G. Simple sequence repeats as advantageous mutators in evolution. Trends Genet. 2006, 22:253-259.
17. Kashi Y., King D.G., Soller M. Simple sequence repeats as a source of quantitative genetic variation. Trends Genet. 1997, 13:74-78.
18. 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.
19. 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.
20. King D.G., Soller M., Kashi Y. Evolutionary tuning knobs. Endeavour 1997, 21:36-40.
21. King A.N., Adams N.J., Carstens E.B., Lefkowitz E.J. Virus taxonomy: classification and nomenclature of viruses. Ninth Report of the International Committee on Taxonomy of Viruses, San Diego 2012.
22. Krupovic M., Koonin E.V. Evolution of eukaryotic single- stranded DNA viruses of Bidnaviridae family from genes of four other groups of widely different viruses. Sci. Rep. 2014, 4:5347.
23. Kumpatla S.P., Mukhopadhyay S. Mining and survey of simple sequence repeats in expressed sequence tags of dicotyledonous species. Genome 2005, 48:985-998.
24. Labonté J., Suttle C.A. Previously unknown and highly divergent ssDNA viruses populate the oceans. ISME J. 2013, 7:2169-2177.
25. Leclercq S., Rivals E., Jarne P. DNA slippage occurs at microsatellite loci without minimal threshold length in humans: a comparative genomic approach. Genome Biol. Evol. 2010, 2:325-335.
26. Li Y.C., Korol A.B., Fahima T., Nevo E. Microsatellites within genes: structure, function, and evolution. Mol. Biol. Evol. 2004, 21:991-1007.
27. Loire E., Higuet D., Netter P., Achaz G. Evolution of coding microsatellites in primate genomes. Genome Biol. Evol. 2013, 5:283-295.
28. López-Bueno A., Villarreal L.P., Almendral J.M. Parvovirus variation for disease: a difference with RNA viruses?. Curr. Top. Microbiol. Immunol. 2006, 299:349-370.
29. Martin D.P., Philippe Biagini P., Lefeuvre P., Golden M., Roumagnac P., Varsani A. Recombination in eukaryotic single stranded viruses. Viruses 2011, 3:1699-1738.
30. Mrazek J., Guo X., Shah A. Simple sequence repeats in prokaryotic genomes. Proc. Natl. Acad. Sci. U. S. A. 2007, 104:8472-8477.
31. Rocha E.P.C. An appraisal of the potential for illegitimate recombination in bacterial genomes and its consequences: from duplications to genome reduction. Genome Res. 2003, 13:1123-1132.
32. Roorkiwal M., Sharma P.C. Mining functional microsatellite in legume unigenes. Bioinformation 2011, 7:264-270.
33. Schlötterer C., Tautz D. Slippage synthesis of simple sequence DNA. Nucleic Acids Res. 1992, 20:211-215.
34. Shackelton L.A., Holmes E.C. Phylogenetic evidence for the rapid evolution of human B19 erythrovirus. J. Virol. 2006, 80:3666-3669.
35. Sharma P.C., Grover A., Kahl G. Mining microsatellites in eukaryotic genomes. Trends Biotechnol. 2007, 25:490-498.
36. Singh A.K., Alam C.M., Sharfuddin C., Ali S. Frequency and distribution of simple and compound microsatellites in forty-eight human papillomavirus (HPV) genomes. Infect. Genet. Evol. 2014, 24:92-98.
37. Suttle C.A. The viriosphere: the greatest biological diversity on Earth and driver of global processes. Environ. Microbiol. 2005, 4:481-482.
38. Thiel T., Michalek W., Varshney R.K., Graner A. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor. Appl. Genet. 2003, 106:411-422.
39. Tóth G., Gáspári Z., Jurka J. Microsatellites in different eukaryotic genomes: survey and analysis. Genome Res. 2000, 10:967-981.
40. Walt E.V., Martin D.P., Varsani A., Polston J.E., Rybicki E.P. Experimental observations of rapid Maize streak virus evolution reveal a strand-specific nucleotide substitution bias. Virol. J. 2008, 5:104.
41. Xu X., Peng M., Fang Z., Xu X. The direction of microsatellite mutations is dependent upon allele length. Nat. Genet. 2000, 24:396-399.
42. Zhao X., Tian Y., Yang R., Feng H., Ouyang Q., Tian Y., Tan Z., Li M., Niu Y., Jiang J., Shen G., Yu R. Co evolution between simple sequence repeats (SSRs) and virus genome size. BMC Genomics 2012, 13:435.
43. Zhao X., Tan Z., Feng H., Yang R., Li M., Jiang J., Shen G., Yu R. Microsatellites in different Potyvirus genomes: survey and analysis. Gene 2011, 488:52-56.