Genome variability and gene content in chordopoxviruses: Dependence on microsatellites

Viruses

Volumn 7, Issue 4, 2015, Pages 2126-2146

  Hatcher, Eneida L ^a   Wang, Chunlin ^b   Lefkowitz, Elliot J ^a  

^a University of Alabama at Birmingham   (United States)

^b STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Early stop mutations; Genome variability; Genomic evolution; Microsatellites; Poxviruses

Indexed keywords

MICROSATELLITE DNA; STOP CODON;

ARTICLE; AVIPOXVIRUS; CANARYPOX VIRUS; CAPRIPOXVIRUS; CERVIDPOXVIRUS; CHORDOPOXVIRINAE; GENE MUTATION; GENETIC ANALYSIS; GENETIC IDENTIFICATION; GENETIC VARIABILITY; LEPORIPOXVIRUS; MOLLUSCIPOXVIRUS; MYXOMA VIRUS; NONSENSE MUTATION; NUCLEOTIDE SEQUENCE; ORTHOPOXVIRUS; PARAPOXVIRUS; SIMPLE SEQUENCE REPEAT; SUIPOXVIRUS; VIRUS GENE; VIRUS GENOME; YATAPOXVIRUS; BIOLOGY; GENE DELETION; GENETIC VARIATION; GENETICS; GENOMIC INSTABILITY; MOLECULAR EVOLUTION; STOP CODON;

CHORDOPOXVIRINAE; POXVIRIDAE;

CHORDOPOXVIRINAE; CODON, NONSENSE; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENE DELETION; GENETIC VARIATION; GENOME, VIRAL; GENOMIC INSTABILITY; MICROSATELLITE REPEATS;

EID: 84928978308     PISSN: 19994915     EISSN: 19994915     Source Type: Journal    
DOI: 10.3390/v7042126     Document Type: Article

References (51)

1. International Committee on Taxonomy of Viruses. Virus Taxonomy: Classification and Nomenclature of Viruses: Ninth Report of the International Committee on Taxonomy of Viruses; Elsevier Academic Press: London, UK, 2011.
2. Carroll, D.S.; Emerson, G.L.; Li, Y.; Sammons, S.; Olson, V.; Frace, M.; Nakazawa, Y.; Czerny, C.P.; Tryland, M.; Kolodziejek, J., et al. Chasing jenner's vaccine: Revisiting cowpox virus classification. PLOS ONE 2011, 6, e23086.
3. Zhao, G.; Droit, L.; Tesh, R.B.; Popov, V.L.; Little, N.S.; Upton, C.; Virgin, H.W.; Wang, D. The genome of yoka poxvirus. J. Virol. 2011, 85, 10230-10238.
4. Hendrickson, R.C.; Wang, C.; Hatcher, E.L.; Lefkowitz, E.J. Orthopoxvirus genome evolution: The role of gene loss. Viruses 2010, 2, 1933-1967.
5. Schramm, B.; Locker, J.K. Cytoplasmic organization of poxvirus DNA replication. Traffic 2005, 6, 839-846.
6. Moss, B. Poxvirus DNA replication. Cold Spring Harb. Perspect. Biol. 2013, 5, a010199.
7. Lefkowitz, E.J.; Wang, C.; Upton, C. Poxviruses: Past, present and future. Virus Res. 2006, 117, 105-118.
8. McLysaght, A.; Baldi, P.F.; Gaut, B.S. Extensive gene gain associated with adaptive evolution of poxviruses. Proc. Natl. Acad. Sci. USA 2003, 100, 15655-15660.
9. Essbauer, S.; Pfeffer, M.; Meyer, H. Zoonotic poxviruses. Vet. Microbiol. 2010, 140, 229-236.
10. Smith, G.L. Genus Orthopoxvirus: Vaccinia virus. In Poxviruses; Mercer, A.A., Weber, O., Schmidt, A., Eds.; Birkhäuser Verlag: Basel, Switzerland, 2007; pp. 1-45.
11. Emerson, G.L.; Li, Y.; Frace, M.A.; Olsen-Rasmussen, M.A.; Khristova, M.L.; Govil, D.; Sammons, S.A.; Regnery, R.L.; Karem, K.L.; Damon, I.K., et al. The phylogenetics and ecology of the orthopoxviruses endemic to north america. PLOS ONE 2009, 4, e7666.
12. Weli, S.C.; Tryland, M. Avipoxviruses: Infection biology and their use as vaccine vectors. Virol. J. 2011, 8, e49.
13. Mockett, B.; Binns, M.M.; Boursnell, M.E.; Skinner, M.A. Comparison of the locations of homologous fowlpox and vaccinia virus genes reveals major genome reorganization. J. Gen. Virol. 1992, 73, 2661-2668.
14. Tulman, E.R.; Afonso, C.L.; Lu, Z.; Zsak, L.; Kutish, G.F.; Rock, D.L. Genome of lumpy skin disease virus. J. Virol. 2001, 75, 7122-7130.
15. Afonso, C.L.; Tulman, E.R.; Lu, Z.; Zsak, L.; Osorio, F.A.; Balinsky, C.; Kutish, G.F.; Rock, D.L. The genome of swinepox virus. J. Virol. 2002, 76, 783-790.
16. Bracht, A.J.; Armien, A.G.; Carrillo, C.; O'Hearn, E.S.; Fabian, A.W.; Moran, K.E.; Lu, Z.; Ariyakumer, D.S.; Rasmussen, J.M.; Metwally, S.A. Isolation and characterization of a cervidpoxvirus from a goitered gazelle (gazella subgutturosa) from a zoologic park in minnesota. J. Zoo Wildl. Med. 2013, 44, 589-595.
17. Darby, A.C.; McInnes, C.J.; Kjaer, K.H.; Wood, A.R.; Hughes, M.; Martensen, P.M.; Radford, A.D.; Hall, N.; Chantrey, J. Novel host-related virulence factors are encoded by squirrelpox virus, the main causative agent of epidemic disease in red squirrels in the UK. PLOS ONE 2014, 9, e96439.
18. MacNeil, A.; Lederman, E.; Reynolds, M.G.; Ragade, N.J.; Talken, R.; Friedman, D.; Hall, W.; Shwe, T.; Li, Y.; Zhao, H., et al. Diagnosis of bovine-associated parapoxvirus infections in humans: Molecular and epidemiological evidence. Zoonoses Public Health 2010, 57, e161-e164.
19. Afonso, C.L.; Delhon, G.; Tulman, E.R.; Lu, Z.; Zsak, A.; Becerra, V.M.; Zsak, L.; Kutish, G.F.; Rock, D.L. Genome of deerpox virus. J. Virol. 2005, 79, 966-977.
20. Hanson, D.; Diven, D.G. Molluscum contagiosum. Dermatol. Online J. 2003, 9, e2.
21. Afonso, C.L.; Tulman, E.R.; Delhon, G.; Lu, Z.; Viljoen, G.J.; Wallace, D.B.; Kutish, G.F.; Rock, D.L. Genome of crocodilepox virus. J. Virol. 2006, 80, 4978-4991.
22. Li, Y.; Carroll, D.S.; Gardner, S.N.; Walsh, M.C.; Vitalis, E.A.; Damon, I.K. On the origin of smallpox: Correlating variola phylogenics with historical smallpox records. Proc. Natl. Acad. Sci. USA 2007, 104, 15787-15792.
23. Likos, A.M.; Sammons, S.A.; Olson, V.A.; Frace, A.M.; Li, Y.; Olsen-Rasmussen, M.; Davidson, W.; Galloway, R.; Khristova, M.L.; Reynolds, M.G., et al. A tale of two clades: Monkeypox viruses. J. Gen. Virol. 2005, 86, 2661-2672.
24. Drake, J.W.; Hwang, C.B. On the mutation rate of herpes simplex virus type 1. Genetics 2005, 170, 969-970.
25. Duffy, S.; Shackelton, L.A.; Holmes, E.C. Rates of evolutionary change in viruses: Patterns and determinants. Nat. Rev. Genet. 2008, 9, 267-276.
26. Odom, M.R.; Hendrickson, R.C.; Lefkowitz, E.J. Poxvirus protein evolution: Family wide assessment of possible horizontal gene transfer events. Virus Res. 2009, 144, 233-249.
27. Hatcher, E.L.; Hendrickson, R.C.; Lefkowitz, E.J. Identification of nucleotide-level changes impacting gene content and genome evolution in orthopoxviruses. J. Virol. 2014, 88, 13651-13668.
28. Schlotterer, C. Evolutionary dynamics of microsatellite DNA. Chromosoma 2000, 109, 365-371.
29. Behe, M.J. Tracts of adenosine and cytidine residues in the genomes of prokaryotes and eukaryotes. DNA Seq. 1998, 8, 375-383.
30. 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.
31. Coenye, T.; Vandamme, P. Characterization of mononucleotide repeats in sequenced prokaryotic genomes. DNA Res. 2005, 12, 221-233.
32. Ellegren, H. Microsatellites: Simple sequences with complex evolution. Nat. Rev. Genet. 2004, 5, 435-445.
33. Moxon, E.R.; Rainey, P.B.; Nowak, M.A.; Lenski, R.E. Adaptive evolution of highly mutable loci in pathogenic bacteria. Curr. Biol. 1994, 4, 24-33.
34. Toth, G.; Gaspari, Z.; Jurka, J. Microsatellites in different eukaryotic genomes: Survey and analysis. Genome Res. 2000, 10, 967-981.
35. Kaufer, B.B.; Jarosinski, K.W.; Osterrieder, N. Herpesvirus telomeric repeats facilitate genomic integration into host telomeres and mobilization of viral DNA during reactivation. J. Exp. Med. 2011, 208, 605-615.
36. Baroudy, B.M.; Moss, B. Sequence homologies of diverse length tandem repetitions near ends of vaccinia virus genome suggest unequal crossing over. Nucleic Acids Res. 1982, 10, 5673-5679.
37. Jain, A.; Mittal, N.; Sharma, P.C. Genome wide survey of microsatellites in ssdna viruses infecting vertebrates. Gene 2014, 552, 209-218.
38. George, B.; Mashhood Alam, C.; 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.
39. 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.
40. Chen, M.; Tan, Z.; Zeng, G. Microsatellite is an important component of complete hepatitis c virus genomes. Infect. Genet. Evol. 2011, 11, 1646-1654.
41. 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.
42. Mudunuri, S.B.; Nagarajaram, H.A. Imex: Imperfect microsatellite extractor. Bioinformatics 2007, 23, 1181-1187.
43. Szpara, M.L.; Tafuri, Y.R.; Parsons, L.; Shamim, S.R.; Verstrepen, K.J.; Legendre, M.; Enquist, L.W. A wide extent of inter-strain diversity in virulent and vaccine strains of alphaherpesviruses. PLOS Pathog. 2011, 7, e1002282.
44. Viral Bioinformatics Resource Center. Available online: www.vbrc.org (accessed on 5 June 2008).
45. Katoh, K.; Misawa, K.; Kuma, K.; Miyata, T. Mafft: A novel method for rapid multiple sequence alignment based on fast fourier transform. Nucleic Acids Res. 2002, 30, 3059-3066.
46. Bratke, K.A.; McLysaght, A. Identification of multiple independent horizontal gene transfers into poxviruses using a comparative genomics approach. BMC Evol. Biol. 2008, 8, e67.
47. Ouyang, Q.; Zhao, X.; Feng, H.; Tian, Y.; Li, D.; Li, M.; Tan, Z. High gc content of simple sequence repeats in herpes simplex virus type 1 genome. Gene 2012, 499, 37-40.
48. Tulman, E.R.; Afonso, C.L.; Lu, Z.; Zsak, L.; Kutish, G.F.; Rock, D.L. The genome of canarypox virus. J. Virol. 2004, 78, 353-366.
49. Elde, N.C.; Child, S.J.; Eickbush, M.T.; Kitzman, J.O.; Rogers, K.S.; Shendure, J.; Geballe, A.P.; Malik, H.S. Poxviruses deploy genomic accordions to adapt rapidly against host antiviral defenses. Cell 2012, 150, 831-841.
50. Martin, D.P.; Biagini, P.; Lefeuvre, P.; Golden, M.; Roumagnac, P.; Varsani, A. Recombination in eukaryotic single stranded DNA viruses. Viruses 2011, 3, 1699-1738.
51. Krupovic, M.; Koonin, E.V. Evolution of eukaryotic single-stranded DNA viruses of the bidnaviridae family from genes of four other groups of widely different viruses. Sci. Rep. 2014, 4, 5347.