Populations of plant viruses are genetically heterogeneous. This heterogeneity is often linked to mutation, the ultimate source of genetic variation and an uncontested player in plant virus evolution. This review gives basic key information indispensable to understanding mutation in plant viruses, from mutation sources, mutation detection means, to the role of mutation in shaping plant virus evolution in combination with various other evolutionary factors. From information drawn from the recent literature, we confirm or refute some generally held views and we reinstate several unanswered questions. It is clear that low genetic diversity characterizes some plant virus populations, irrespective of their life cycle or their nature (DNA or RNA). Mutation frequencies of plant DNA viruses can be as high as those of RNA viruses. This casts some doubt on a positive correlation between high mutation rates and adaptive evolution, and on the lack of proofreading for RNAdependent RNA polymerases. However, the lack of information on viral mutation rates still precludes a complete understanding of the link between mutation rates and population heterogeneity. Information about plant virus replication mode, generation time and generation size also is still crucially needed before a complete picture of virus evolution will emerge.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Ali A, Li H, Schneider WL, Sherman DJ, Gray S, Smith D, Roossinck MJ (2006) Analysis of genetic bottlenecks during horizontal transmission of Cucumber mosaic virus. J Virol 80(17):8345–8350
Aranda MA, Fraile A, Garcia-Arenal F, Malpica J (1995) Experimental evaluation of the ribonuclease protection assay method for the assessment of genetic heterogeneity in populations of RNA viruses. Arch Virol 140:1373–1383
Bass BL (2002) RNA editing by adenosine deaminases that act on RNA. Annu Rev Biochem 71(1):817–846
Bierne H, Vilette D, Ehrlich S, Michel B (1997) Isolation of a dnaE mutation which enhances RecA-independent homologous recombination in the Escherichia coli chromosome. Mol Biol 24(6):1225–1234
Bisaro DM (1996) Geminivirus DNA replication. In: DePamphilis ML (ed) DNA Replication in eukaryotic cells. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, pp 833–854
Bull JJ, Ancel ML, Lachmann M (2005) Quasispecies made simple. PLoS Biol 1(6):450–460
Burch CL, Chao L (2000) Evolvability of an RNA virus is determined by its mutational neighbourhood. Nature 406(10):625–628
Chao L, Rang CU, Wong, LE (2002) Distribution of spontaneous mutants and inferences about the replication mode of the RNA bacteriophage ø6. J Virol 76(7):3276–3281
Cheng C-P, Nagy PD (2003) Mechanism of RNA recombination in carmo- and tombusviruses: evidence for template switching by the RNA-dependent RNA polymerase in vitro. J Virol 77(22):12033–12047
Cuevas JM, Moya A, Sanjuan R (2005) Following the very initial growth of biological RNA viral clones. J Gen Virol 86(2):435–443
Domingo E (2002) Quasispecies theory in virology. J Virol 76(1):463–465
Domingo E Holland JJ (1994) Mutation rates and rapid evolution of RNA viruses. In: Morse SS (ed) The evolutionary biology of viruses. Raven, New York, pp 161–184
Domingo E, Holland JJ (1997) RNA virus mutations and fitness for survival. Annu Rev Microbiol 51:151–178
Drake JW (1991) A constant rate of spontaneous mutation in DNA-based microbes. Proc Natl Acad Sci USA 88:7160–7164
Drake JW (1993) Rates of spontaneous mutation among RNA viruses. Proc Natl Acad Sci USA 90:4171–4175
Drake JW, Holland JJ (1999) Mutation rates among RNA viruses. Proc Natl Acad Sci USA 96(24):13910–13913
Drake JW, Hwang CBC (2005) On the mutation rate of herpes simplex virus type I. Genetics 170:969–970
Drake JW, Charlesworth B, Charlesworth D, Crow JF (1998) Rates of spontaneous mutation. Genetics 148:1667–1686
Dwyer GI, Gibbs MJ, Gibbs AJ, Jones RAC (2007) Wheat streak mosaic virus in Australia: relationship to isolates from the Pacific northwest of the USA and its dispersion via seed transmission. Plant Dis 91(2):164–170
Fields BN, Joklik, WK (1969) Isolation and preliminary genetic and biochemical characterization of temperature-sensitive mutants of reovirus. Virology 37:335–342
French R, Stenger DC (2003) Evolution of Wheat streak mosaic virus: dynamics of population growth within plants may explain limited variation. Annu Rev Phytopathol 41:199–214
Furió V, Moya A, Sanjuan R (2005) The cost of replication fidelity in an RNA virus. Proc Natl Acad Sci USA 102(69):10233–10237
GarcÃa-Arenal F, Fraile A, Malpica J (2003) Variation and evolution of plant virus populations. Int Microbiol 6:225–232
GarcÃa-Arenal F, Fraile A, Malpica JM (2001) Variability and genetic structure of plant virus populations. Annu Rev Phytopathol 39:157–186
Ge L, Zhang J, Zhou X, Li H (2007) Genetic structure and population variability of tomato yellow leaf curl China virus. J Virol 81(11):5902–5907
Gierer A, Mundry K-W (1958) Production of mutants of tobacco mosaic virus by chemical alteration of its ribonucleic acid in vitro. Nature 182(4647):1457–1458
Grogan DW, Carver GT, Drake JW (2001) Genetic fidelity under harsh conditions: analysis of spontaneous mutation in the thermoacidophilic archaeon Sulfolobus acidocaldarius. Proc Natl Acad Sci USA 98(14):7928–7933
Hall G (2006) Selective constraint and genetic differentiation in geographically distant barley yellow dwarf virus populations. J Gen Virol 87(10):3067–3075
Halle S (1968) 5-Azacytidine as a mutagen for arboviruses. J Virol 2(10):1228–1229
Hancock JM, F Santibáñez-Koref MF (1998) Trinucleotide expansion disease in the context of micro- and minisatellite evolution, Hammersmith Hospital, April 1–3, 1998. EMBO J 17(19):5521–5524
Hancock JM, Chaleeprom W, Chaleeprom W, Dale J, Gibbs A (1995) Replication slippage in the evolution of potyviruses. J Gen Virol 76:3229–3232
Hanley-Bowdoin L, Settlage SB, Orozco BM, Nagar S Robertson D (1999) Geminiviruses: models for plant DNA replication, transcription, and cell cycle regulation. Crit Rev Plant Sci 18(1):71–106
Holland JJ, Domingo E, de la Torre JC, Steinhauer DA (1990) Mutation frequencies at defined single codon sites in vesicular stomatitis virus and poliovirus can be increased only slightly by chemical mutagenesis. J Virol 64(8):3960–3962
Holmes EC, Moya A (2002) Is the quasispecies concept relevant to RNA viruses? J Virol 76(1):460–462
Inamdar NM, Zhang X-Y, Brough CL, Gardiner WE, Bisaro DM, Ehrlich M (1992) Transfection of heteroduplexes containing uracil-guanine or thymine-guanine mispairs into plant cells. Plant Mol Biol 20:123–131
Isnard M, Granier M, Frutos R, Reynaud B, Peterschmitt M (1998) Quasispecies nature of three maize streak virus isolates obtained through different modes of selection from a population used to assess response to infection of maize cultivars. J Gen Virol 79:3091–3099
Koenig RP, Luddecke P, Haeberle AM (1995) Detection of been necrotic yellow vein virus strains, variants and mixed infections by examining single-stranded conformation polymorphisms on immunocaptured RT-PCR products. J Gen Virol 76:2051–2055
Kunkel LO (1947) Variation in phytopathogenic viruses. Annu Rev Microbiol 1:85–100
Li H, Roossinck, MJ (2004). Genetic bottlenecks reduce population variation in an experimental RNA virus population. J Virol 78(19):10582–10587
Lin H-X, Rubio L, Smythe AB, Falk BW (2004) Molecular population genetics of Cucumber mosaic virus in California: evidence for founder effects and reassortment. J Virol 78(12):6666–6675
Luria SE, Delbruck M (1943) Mutations of bacteria from virus sensitivity to virus resistance. Genetics 28:491–511
Malpica JM, Fraile A, Moreno I, Obies CI, Drake JW, GarcÃa-Arenal F (2002) The rate and character of spontaneous mutations in an RNA virus. Genetics 162:1505–1511
Martin DP, Willment JA, Billharz R, Velders R, Odhiambo B, Njuguna J, James D, Rybicki EP (2001) Sequence diversity and virulence in Zea mays of Maize streak virus isolates. Virology 288(2):247–255
Martin S, Garcia ML, Troisi A, Rubio L, Legarreta G, Grau O, Alioto D, Moreno P, Guerri J (2006) Genetic variation of populations of Citrus psorosis virus. J Gen Virol 87(10):3097–3102
Maynard SJ, Szathmary E (1995) The major transitions in evolution. Freeman/Spektrum, Oxford
Nagy PD, Bujarski J (1996) Homologous RNA recombination in brome mosaic virus AU-rich sequences decrease the accuracy of crossovers. J Virol 70(1):415–426
Naraghi-Arani P, Daubert S, Rowhani A (2001) Quasispecies nature of the genome of Grapevine fanleaf virus. J Gen Virol 82:1791–1795
Ndunguru J, Legg J, Aveling T, Thompson G, Fauquet C (2005) Molecular biodiversity of cassava begomoviruses in Tanzania: evolution of cassava geminiviruses in Africa and evidence for East Africa being a center of diversity of cassava geminiviruses. Virol J 2(1):21
Ooi K, Ohshita S, Ishii I, Yahara T (1997) Molecular phylogeny of geminivirus infecting wild plants in Japan. J Plant Res 110(2):247–257
Pathak V, Temin H (1990) Broad spectrum of in vivo forward mutations, hypermutations, and mutational hotspots in a retroviral shuttle vector after a single replication cycle: substitutions, frameshifts, and hypermutations. Proc Natl Acad Sci 87(16):6019–6023
Pathak VK, Temin HM (1992) 5-Azacytidine and RNA secondary structure increase the retrovirus mutation rate. J Virol 66(5):3093–3100
Pennington RE, Melcher U (1993) In planta deletion of DNA inserts from the large intergenic region of Califlower mosaic virus DNA. Virology 192:188–196
Pita JS, de Miranda JR, Schneider WL, Roossinck MJ (2007) Environment determines fidelity for an RNA virus replicase. J Virol 81(17):9072–9077
Pita JS, Fondong VN, Sangaré A, Otim-Nape GW, Ogwal S, Fauquet CM (2001) Recombination, pseudorecombination and synergism of geminiviruses are determinant keys to the epidemic of severe cassava mosaic disease in Uganda. J Gen Virol 82:655–665
Polson AG, Bass BL, Casey JL (1996) RNA editing of hepatitis delta virus antigenome by dsRNA adenosine deaminase. Nature 380:454–456
Pringle CR (1970) Genetic characteristics of conditional lethal mutants of vesicular stomatitis virus induced by 5-fluorouracil, 5-azacytidine, and ethyl methane sulfonate. J Virol 5(5):559–567
RodrÃguez-Alvarado G, Roossinck MJ (1997) Structural analysis of a necrogenic strain of cucumber mosaic cucumovirus satellite RNA in planta. Virology 236:155–166
Roossinck MJ (1997) Mechanisms of plant virus evolution. Ann Rev Phytopathol 35:191–209
Roossinck MJ, Ali A (2007) Mechanisms of plant virus evolution and identification of genetic bottlenecks: impact on disease management. In: Punja ZK, DeBoer SH, Sanfaçon H (eds) Biotechnology and plant disease management. CABI, Wallingford, pp 109–124
Roossinck MJ, Schneider WL (2005) Mutant clouds and occupation of sequence space in plant RNA viruses. In: Domingo E (ed) Quasispecies: concepts and implications for virology. Current topics in microbiology and immunology, vol 299. Springer, Heidelberg, pp 337–348
Rosenberg SM (2001) Evolving responsively: adaptive mutation. Nat Rev Genet 2:504–515
Sanchez-Campos S, Diaz JA, Monci F, Bejarano ER, Reina J, Vavas-Castillo MA, Aranda MA, Moriones E (2002) High genetic stability of the begomovirus Tomato yellow leaf curl Sardinia virus in southern Spain over an 8-year period. Phyopathology 92(8):842–849
Sanz AI, Fraile A, Gallego JM, Malpica JM, GarcÃa-Arenal F (1999). Genetic variability of natural populations of Cotton leaf curl geminivirus, a single-stranded DNA virus. J Mol Evol 49(5):672–681
Schalk H-J, Matzeit V, Schiller B, Schell J, Gronenborn B (1989) Wheat dwarf virus, a geminivirus of graminaceous plants needs splicing for replication. EMBO J 8(2):359–364
Schneider WL, Roossinck MJ (2000) Evolutionarily related sindbis-like plant viruses maintain different levels of population diversity in a common host. J Virol 74(7):3130–3134
Schneider WL, Roossinck MJ (2001) Genetic diversity in RNA viral quasispecies is controlled by host-virus interactions. J Virol 75(14):6566–6571
Scholthof H, Wu FC, Richins RD, Shepherd RJ (1991) A naturally occurring deletion mutant of Figwort mosaic virus (caulimovirus) is generated by RNA splicing. Virology 184:290–298
Scott J (1995) A place in the world for RNA editing. Cell 81:833–836
Smith DB, Inglis SC (1987) The mutation rate and variability of eukaryotic viruses: an analytical review. J Gen Virol 68(11):2729–2740
Steinhauer DA, Holland JJ (1986) Direct method for quantification of extreme polymerase error frequencies at selected single base sites in viral RNA. J Virol 57:219–228
Teycheney P-Y, Laboureau N, Iskra-Caruana M-L, Candresse T (2005) High genetic variability and evidence for plant-to-plant transfer of Banana mild mosaic virus. J Gen Virol 86:3179–3187
Vadivukarasi T, Girish KR, Usha R (2007) Sequence and recombination analyses of the geminivirus replication initiator protein. J Biosci 32(1):17–29
Vignuzzi M, Stone JK, Arnold JJ, Cameron CE, Andino R (2006) Quasispecies diversity determines pathogenesis through cooperative interactions in a viral population. Nature 439:344–348
Viguera E, Canceill D, Ehrlich SD (2001) Replication slippage involves DNA polymerase pausing and dissociation. EMBO J 20(10):2587–2595
Wang H, Huang LF, Cooper JI (2006) Analyses on mutation patterns, detection of population bottlenecks, and suggestion of deleterious-compensatory evolution among members of the genus Potyvirus. Arch Virol 151(8):1625–1633
Yarwood CE (1979) Host passage effects with plant viruses. Adv Virus Res 24:69–90
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2008 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Pita, J.S., Roossinck, M.J. (2008). Virus Populations, Mutation Rates and Frequencies. In: Roossinck, M.J. (eds) Plant Virus Evolution. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-75763-4_6
Download citation
DOI: https://doi.org/10.1007/978-3-540-75763-4_6
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-75762-7
Online ISBN: 978-3-540-75763-4
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)