Skip to main content
SpringerLink
Log in
Book cover

Population Genomics: Microorganisms pp 233–265Cite as

Population Genomics of Plant Viruses

  • Chapter
  • First Online:

Part of the book series: Population Genomics ((POGE))

Abstract

For more than one century, studies of plant viruses have broken paths in many fields of biology. More recently, studies of plant viruses have also been pioneer in population genomics. In the past few decades, there has been a significant advance in the number, sophistication, and quality of molecular techniques and bioinformatics tools for the genetic characterization of virus populations. This has broadened current knowledge on the mechanisms that generate genetic diversity and on the evolutionary forces and ecological factors that shape the genetic structure and dynamics of plant virus populations. This chapter aims at summarizing this knowledge, and it is structured around three major levels at which plant virus populations have been studied:

  1. 1.

    The within-host level, that is, the analysis of the genetic diversity of virus populations during plant colonization and of how phenomena such as co-/superinfection exclusion and population bottlenecks determine population structure

  2. 2.

    The between-host level, which includes studies on genetic diversity of virus populations in the host plant population and on the ecological factors shaping the genetic structure of the virus populations

  3. 3.

    The community level, which adddresses current studies on the genetic diversity of virus communities in multiple infected hosts and of multi-host-multivirus interactions

In sum, we provide an overview of current understanding on the population genomics of plant viruses at every level of population organization.

This is a preview of subscription content, log in via an institution.

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD   199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

References

  • Acosta-Leal R, Duffy S, Xiong Z, Hammond RW, Elena SF. Advances in plant virus evolution: translating evolutionary insights into better disease management. Phytopathology. 2011;101:1136–48.

    CAS  PubMed  Google Scholar 

  • Agnew P, Koella JC, Michalakis Y. Host life-history responses to parasitism. Microbes Infect. 2000;2:891–6.

    CAS  PubMed  Google Scholar 

  • Alí A, Roossinck MJ. Genetic bottlenecks during systemic movement of Cucumber mosaic virus vary in different host plants. Virology. 2010;404:279–83.

    PubMed  Google Scholar 

  • Almeida RPP, Bennett GM, Anhalt MD, Tsai C-W, O’Grady P. Spread of an introduced vector-borne banana virus in Hawaii. Mol Ecol. 2009;18:136–46.

    PubMed  Google Scholar 

  • de Assis Filho F, Sherwood J. Evaluation of seed transmission of turnip yellow mosaic virus and tobacco mosaic virus in Arabidopsis thaliana. Phytopathology. 2000;90:1233–8.

    PubMed  Google Scholar 

  • Bedhomme S, Agnew P, Vital Y, Sidobre C, Michalakis Y. Prevalence-dependent costs of parasite virulence. PLoS Biol. 2005;2:e262.

    Google Scholar 

  • Bergua M, Zwart MP, El-Mohtar C, Shilts T, Elena SF, Folimonova SY. A viral protein mediates superinfection exclusion at the whole-organism level but is not required for exclusion at the cellular level. J Virol. 2014;88:11327–38.

    PubMed  PubMed Central  Google Scholar 

  • Berzal-Herranz A, de la Cruz A, Tenllado F, Díaz-Ruíz JR, López L, Sanz AI, Vaquero C, Serra MT, García-Luque I. The Capsicum L 3 gene-mediated resistance against the tobamoviruses is elicited by the coat protein. Virology. 1995;209:498–505.

    CAS  PubMed  Google Scholar 

  • Blawid R, Silva JMF, Nagata T. Discovering and sequencing new plant viral genomes by next-generation sequencing: description of a practical pipeline. Ann Appl Biol. 2017;170:301–14.

    Google Scholar 

  • Blok J, Mackenzie A, Guy P, Gibbs AJ. Nucleotide sequence comparisons of turnip yellow mosaic isolates from Australia and Europe. Arch Virol. 1987;97:283–95.

    CAS  PubMed  Google Scholar 

  • Borer ET, Adams VT, Engler GA, Adams AL, Schumann CB, Seabloom EW. Aphid fecundity and grassland invasion: invader life history is the key. Ecol Appl. 2009;19:1187–96.

    PubMed  Google Scholar 

  • Borer ET, Seabloom EW, Mitchell CE, Power AG. Local context drives infection of grasses by vector-borne generalist viruses. Ecol Lett. 2010;13:810–8.

    PubMed  Google Scholar 

  • Bujarski J. Genetic recombination in plant-infecting messenger-sense RNA viruses: overview and research perspectives. Front Plant Sci. 2013;4:68.

    PubMed  PubMed Central  Google Scholar 

  • Burdon JJ, Chilvers GA. Host density as a factor in plant-disease ecology. Annu Rev Phytopathol. 1982;20:143–66.

    Google Scholar 

  • Burdon JJ, Thrall PH. Pathogen evolution across the agro-ecological interface: implications for disease management. Evol Appl. 2008;1:57–65.

    PubMed  PubMed Central  Google Scholar 

  • Carrasco P, de la Iglesia F, Elena SF. Distribution of fitness and virulence effects caused by single-nucleotide substitutions in tobacco etch virus. J Virol. 2007;81:12979–84.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Chao L. Fitness of RNA virus decreased by Muller’s ratchet. Nature. 1990;348:454–5.

    CAS  PubMed  Google Scholar 

  • Chao L. Levels of selection, evolution of sex in RNA viruses, and the origin of life. J Theor Biol. 1991;153:229–46.

    CAS  PubMed  Google Scholar 

  • Chen S, Huang Q, Wu L, Qian Y. Identification and characterization of a maize-associated mastrevirus in China by deep sequencing small RNA populations. Virol J. 2015;12:156.

    PubMed  PubMed Central  Google Scholar 

  • Clarke DD. Tolerance of parasites and disease in plants and its significance in host-parasite interactions. Adv Plant Pathol. 1986;5:161–98.

    Google Scholar 

  • Coetzee B, Freeborough M-J, Maree HJ, Celton J-M, Rees DJG, Burger JT. Deep sequencing analysis of viruses infecting grapevines: virome of a vineyard. Virology. 2010;400:157–63.

    CAS  PubMed  Google Scholar 

  • De Bruyn A, Villemot J, Lefeuvre P, Villar E, Hoareau M, Harimalala M, Abdoul-Karime AL, Abdou-Chakour C, Reynaud B, Harkins GW, Varsani A, Martin DP, Lett JM. East African cassava mosaic-like viruses from Africa to Indian Ocean islands: molecular diversity, evolutionary history and geographical dissemination of a bipartite begomovirus. BMC Evol Biol. 2012;12:228.

    PubMed  PubMed Central  Google Scholar 

  • Delwart EL. Viral metagenomics. Rev Med Virol. 2007;17:115–31.

    CAS  PubMed  Google Scholar 

  • Dietrich C, Maiss E. Fluorescent labelling reveals spatial separation of potyvirus populations in mixed infected Nicotiana benthamiana plants. J Gen Virol. 2003;84:2871–6.

    CAS  PubMed  Google Scholar 

  • Divéki Z, Salánki K, Balázs E. Limited utility of blue fluorescent protein in monitoring plant virus movement. Biochimie. 2002;84:997–1002.

    PubMed  Google Scholar 

  • Donaire L, Wang Y, Gonzalez-Ibeas D, Mayer KF, Aranda MA, Llave C. Deep-sequencing of plant viral small RNAs reveals effective and widespread targeting of viral genomes. Virology. 2009;392:203–14.

    CAS  PubMed  Google Scholar 

  • Donaire L, Burgyán J, García-Arenal F. RNA silencing may play a role in but is not the only determinant of the multiplicity of infection. J Virol. 2016;90:553–61.

    CAS  PubMed  Google Scholar 

  • Drake JW, Holland JJ. Mutation rates among RNA viruses. Proc Natl Acad Sci U S A. 1999;96:13910–3.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Drummond AJ, Pybus OG, Rambaut A, Forsberg R, Rodrigo AG. Measurably evolving populations. Trends Ecol Evol. 2003;18:481–8.

    Google Scholar 

  • Duffy S, Holmes EC. Phylogenetic evidence for rapid rates of molecular evolution in the single-stranded DNA begomovirus tomato yellow leaf curl virus. J Virol. 2008;82:957–65.

    CAS  PubMed  Google Scholar 

  • Duffy S, Holmes EC. Validation of high rates of nucleotide substitution in geminiviruses: phylogenetic evidence from East African cassava mosaic viruses. J Gen Virol. 2009;90:1539–47.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Duffy S, Shackelton LA, Holmes EC. Rates of evolutionary change in viruses: patterns and determinants. Nat Rev Genet. 2008;9:267–76.

    CAS  PubMed  Google Scholar 

  • Dunham JP, Simmons HE, Holmes EC, Stephenson AG. Analysis of viral (zucchini yellow mosaic virus) genetic diversity during systemic movement through a Cucurbita pepo vine. Virus Res. 2014;191:172–9.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Elena SF, Sanjuán R. On the adaptive value of high mutation rates in RNA viruses: separating causes from consequences. J Virol. 2005;79:11555–8.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Elena SF, Fraile A, García-Arenal F. Evolution and emergence of plant viruses. Adv Virus Res. 2014;88:161–91.

    CAS  PubMed  Google Scholar 

  • Fabre F, Moury B, Johansen EI, Simon V, Jacquemond M, Senoussi R. Narrow bottlenecks affect Pea seedborne mosaic virus populations during vertical seed transmission but not during leaf colonization. PLoS Pathog. 2014;10:e1003833.

    PubMed  PubMed Central  Google Scholar 

  • Fargette D, Pinel A, Rakotomalala M, Sangu E, Traoré O, Sérémé D, Sorho F, Issaka S, Hébrard E, Séré Y, Kanyeka Z, Konaté G. Rice yellow mottle virus, an RNA plant virus, evolves as rapidly as most RNA animal viruses. J Virol. 2008a;82:3584–9.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Fargette D, Pinel-Galzi A, Sérémé D, Lacombe S, Hébrard E, Traoré O, Konaté G. Diversification of Rice yellow mottle virus and related viruses spans the history of agriculture from the Neolithic to the present. PLoS Pathog. 2008b;4:e1000125.

    PubMed  PubMed Central  Google Scholar 

  • Fawcett HS. The importance of investigations on the effects of known mixtures of microorganisms. Phytopathology. 1931;2:545–50.

    Google Scholar 

  • Fraile A, García-Arenal F. The coevolution of plants and viruses: resistance and pathogenicity. Adv Virus Res. 2010;76:1–32.

    CAS  PubMed  Google Scholar 

  • Fraile A, Pagán I, Anastasio G, Sáez E, García-Arenal F. Rapid genetic diversification and high fitness penalties associated with pathogenicity evolution in a plant virus. Mol Biol Evol. 2011;28:1425–37.

    CAS  PubMed  Google Scholar 

  • Fraile A, Hily J-M, Pagán I, Pacios LF, García-Arenal F. Host resistance selects for traits unrelated to resistance-breaking that affect fitness in a plant virus. Mol Biol Evol. 2014;31:928–39.

    CAS  PubMed  Google Scholar 

  • Fraile A, McLeish MJ, Pagán I, González-Jara P, Piñero P, García-Arenal F. Environmental heterogeneity and the evolution of plant-virus interactions: viruses in wild pepper populations. Virus Res. 2017;241:68–76.

    CAS  PubMed  Google Scholar 

  • Frank SA. Multiplicity of infection and the evolution of hybrid incompatibility in segmented viruses. Heredity. 2001;87:522–9.

    CAS  PubMed  Google Scholar 

  • French R, Stenger DC. Evolution of wheat streak mosaic virus: dynamics of population growth within plants may explain limited variation. Annu Rev Phytopathol. 2003;41:199–214.

    CAS  PubMed  Google Scholar 

  • Friess N, Maillet J. Influence of cucumber mosaic virus infection on the intraspecific competitive ability and fitness of purslane (Portulaca oleracea). New Phytol. 1996;132:103–11.

    Google Scholar 

  • Froissart R, Wilke CO, Montville R, Remold SK, Chao L, Turner PE. Co-infection weakens selection against epistatic mutations in RNA viruses. Genetics. 2004;168:9–19.

    PubMed  PubMed Central  Google Scholar 

  • Froissart R, Roze D, Uzest M, Galibert L, Blanc S, Michalakis Y. Recombination every day: abundant recombination in a virus during a single multi-cellular host infection. PLoS Biol. 2005;3:e89.

    PubMed  PubMed Central  Google Scholar 

  • Froissart R, Doumayrou J, Vuillaume F, Alizon S, Michalakis Y. The virulence-transmission trade-off in vector-borne plant viruses: a review of (non-)existing studies. Philos Trans R Soc B. 2010;365:1907–18.

    CAS  Google Scholar 

  • García-Andrés S, Tomás DM, Sánchez-Campos S, Navas-Castillo J, Moriones E. Frequent occurrence of recombinants in mixed infections of tomato yellow leaf curl disease associated begomoviruses. Virology. 2007;365:210–9.

    PubMed  Google Scholar 

  • García-Arenal F, Fraile A. Questions and concepts in plant virus evolution: a historical perspective. In: Roossinck MJ, editor. Plant virus evolution. Berlin: Springer; 2008. p. 1–14.

    Google Scholar 

  • García-Arenal F, Fraile A. Population dynamics and genetics of plant infection by viruses. In: Caranta C, Aranda MA, Tepfer M, Lopez-Moya JJ, editors. Recent advances in plant virology. Norfolk: Caister Academic Press; 2011. p. 263–81.

    Google Scholar 

  • García-Arenal F, Fraile A. Trade-offs in host range evolution of plant viruses. Plant Pathol. 2013;62:S2–9.

    Google Scholar 

  • García-Arenal F, McDonald BA. An analysis of the durability of resistance to plant viruses. Phytopathology. 2003;93:941–52.

    PubMed  Google Scholar 

  • García-Arenal F, Fraile A, Malpica JM. Variability and genetic structure of plant virus populations. Annu Rev Phytopathol. 2001;39:157–86.

    PubMed  Google Scholar 

  • Ghoshal B, Sanfaçon H. Symptom recovery in virus-infected plants: revisiting the role of RNA silencing mechanisms. Virology. 2015;479–480:167–79.

    PubMed  Google Scholar 

  • Giampetruzzi A, Roumi V, Roberto R, Malossini U, Yoshikawa N, La Notte P, Terlizzi F, Credi R, Saldarelli P. A new grapevine virus discovered by deep sequencing of virus- and viroid-derived small RNAs in Cv Pinot gris. Virus Res. 2012;163:262–8.

    CAS  PubMed  Google Scholar 

  • Gibbs AJ. A plant virus that partially protects its wild legume host against herbivores. Intervirology. 1980;13:42–7.

    CAS  PubMed  Google Scholar 

  • Gibbs AJ, Blok J, Coates DJ, Guy PL, Mackenzie A, Pigram N. Turnip yellow mosaic virus in an endemic Australian alpine Cardamine. In: Barlow BA, editor. Flora and Fauna of Alpine Australasia; ages and origins. Collingwood: CSIRO; 1986. p. 289–300.

    Google Scholar 

  • Gibbs AJ, Gibbs MJ, Ohshima K, García-Arenal F. More plant virus evolution; past present and future. In: Domingo E, Parrish CR, Holland JJ, editors. Origin and evolution of viruses. 2nd ed. London: Academic Press; 2008a.

    Google Scholar 

  • Gibbs AJ, Ohshima K, Phillips MJ, Gibbs MJ. The prehistory of potyviruses: their initial radiation was during the dawn of agriculture. PLoS One. 2008b;3:e2523.

    PubMed  PubMed Central  Google Scholar 

  • Gibbs AJ, Fargette D, García-Arenal F, Gibbs MJ. Time—the emerging dimension of plant virus studies. J Gen Virol. 2010;91:13–22.

    CAS  PubMed  Google Scholar 

  • Gibbs AJ, Wood J, Garcia-Arenal F, Ohshima K, Armstrong JS. Tobamoviruses have probably co-diverged with their eudicotyledonous hosts for at least 110 million years. Virus Evol. 2015;1:vev019.

    PubMed  PubMed Central  Google Scholar 

  • Gibbs AJ, Ohshima K, Yasaka R, Mohammadi M, Gibbs MJ, Jones RAC. The phylogenetics of the global population of potato virus Y and its necrogenic recombinants. Virus Evol. 2017;3:vex002.

    PubMed  PubMed Central  Google Scholar 

  • Gómez P, Sempere RN, Elena SF, Aranda MA. Mixed infections of Pepino mosaic virus strains modulate the evolutionary dynamics of this emergent virus. J Virol. 2009;83:12378–87.

    PubMed  PubMed Central  Google Scholar 

  • Gómez P, Sempere RN, Aranda MA, Elena SF. Phylodynamics of Pepino mosaic virus. Eur J Plant Pathol. 2012;134:445–9.

    Google Scholar 

  • González-Jara P, Fraile A, Canto T, García-Arenal F. The multiplicity of infection of a plant virus varies during colonization of its eukaryotic host. J Virol. 2009;83:7487–94.

    PubMed  PubMed Central  Google Scholar 

  • González-Jara P, Fraile A, Canto T, García-Arenal F. The multiplicity of infection of a plant virus varies during colonization of its eukaryotic host. Author’s correction. J Virol. 2013;87:2374.

    PubMed Central  Google Scholar 

  • Gutiérrez S, Yvon M, Thébaud G, Monsion B, Michalakis Y, Blanc S. Dynamics of the multiplicity of cellular infection in a plant virus. PLoS Pathog. 2010;6:e1001113.

    PubMed  PubMed Central  Google Scholar 

  • Gutiérrez S, Michalakis Y, Blanc S. Virus population bottlenecks during within-host progression and host-to-host transmission. Curr Op Virol. 2012a;2:546–55.

    Google Scholar 

  • Gutiérrez S, Yvon M, Pirolles E, Garzo E, Fereres A, Michalakis Y, Blanc S. Circulating virus load determines the size of bottlenecks in viral populations progressing within a host. PLoS Pathog. 2012b;8:e1003009.

    PubMed  PubMed Central  Google Scholar 

  • Gutiérrez S, Pirolles E, Yvon M, Baecker V, Michalakis Y, Blanc S. The multiplicity of cellular infection changes depending on the route of cell infection in a plant virus. J Virol. 2015;89:9665–75.

    PubMed  PubMed Central  Google Scholar 

  • Guy P, Gibbs AJ. A tymovirus of Cardamine sp. from alpine Australia. Australas Plant Pathol. 1981;10:12–3.

    Google Scholar 

  • Hackett J, Muthukumar V, Wiley GB, Palmer MW, Roe BA, Melcher U. Viruses in Oklahoma Euphorbia marginata. Proc Oklahoma Acad Sci. 2009;89:49–54.

    Google Scholar 

  • Hadidi A, Flores R, Candresse T, Barba M. Next-generation sequencing and genome editing in plant virology. Front Microbiol. 2016;7:1325.

    PubMed  PubMed Central  Google Scholar 

  • Hajimorad MR, Wen R-H, Eggenberger AL, Hill JH, Saghai Maroof MA. Experimental adaptation of an RNA virus mimics natural evolution. J Virol. 2011;85:2557–64.

    CAS  PubMed  Google Scholar 

  • Hall JS, French R, Hein GL, Morris TJ, Stenger DC. Three distinct mechanisms facilitate genetic isolation of sympatric wheat streak mosaic virus lineages. Virology. 2001;282:230–6.

    CAS  PubMed  Google Scholar 

  • Hall GS, Peters JS, Little DP, Power AG. Plant community diversity influences vector behavior and Barley yellow dwarf virus population structure. Plant Pathol. 2010;59:152–1158.

    Google Scholar 

  • Hamada H, Takeuchi S, Kiba A, Tsuda S, Hikichi Y, Okuno T. Amino acid changes in Pepper mild mottle virus coat protein that affect L 3 gene-mediated resistance in pepper. J Gen Plant Pathol. 2002;68:155–62.

    CAS  Google Scholar 

  • Hamada H, Tomita R, Iwadate Y, Kobayashi K, Minemura I, Takeuchi S, Hikichi Y, Suzuki K. Cooperative effect of two amino acid mutations in the coat protein of Pepper mild mottle virus overcomes L 3-mediated resistance in Capsicum plants. Virus Genes. 2007;34:205–14.

    CAS  PubMed  Google Scholar 

  • Harkins GW, Delport W, Duffy S, Wood N, Monjane AL, Owor BE, Donaldson L, Saumtally S, Triton G, Briddon RW, Shepherd DN, Rybicki EP, Martin DP, Varsani A. Experimental evidence indicating that mastreviruses probably did not co-diverge with their hosts. Virol J. 2009;6:104.

    PubMed  PubMed Central  Google Scholar 

  • Harrison BD. The infectivity of extracts made from leaves at intervals after inoculation with viruses. J Gen Microbiol. 1956;15:210–20.

    CAS  PubMed  Google Scholar 

  • Hartl DL, Clark AG. Principles of population genetics. 4th ed. Sunderland: Sinauer; 2007.

    Google Scholar 

  • Hillung J, Cuevas JM, Elena SF. Evaluating the within-host fitness effects of mutations fixed during virus adaptation to different ecotypes of a new host. Philos Trans R Soc B. 2015;370:20140292.

    Google Scholar 

  • Hochberg ME. Population dynamic consequences of the interplay between parasitism and intraspecific competition for host-parasite systems. Oikos. 1991;61:297–306.

    Google Scholar 

  • Holmes EC. The evolution and emergence of RNA viruses. Oxford: Oxford University Press; 2009.

    Google Scholar 

  • Hughes AL. Small effective population sizes and rare nonsynonymous variants in potyviruses. Virology. 2009;393:127–34.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hull R. Plant virology. 5th ed. San Diego: Academic Press; 2014.

    Google Scholar 

  • Hull R, Plaski A. Electron microscopy on the behaviour of two strains of Alfalfa mosaic virus in mixed infections. Virology. 1970;42:773–6.

    CAS  PubMed  Google Scholar 

  • Hurwitz BL, Sullivan MB. The Pacific Ocean virome (POV): a marine viral metagenomic dataset and associated protein clusters for quantitative viral ecology. PLoS One. 2013;8:e57355.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Ishibashi K, Kezuka Y, Kobayashi C, Kato M, Inoue T, Nonaka T, Ishikawa M, Matsumura H, Katoh E. Structural basis for the recognition-evasion arms race between Tomato mosaic virus and the resistance gene Tm-1. Proc Natl Acad Sci U S A. 2014;111:3486–95.

    Google Scholar 

  • Jenkins GM, Rambaut A, Pybus OG, Holmes EC. Rates of molecular evolution in RNA viruses: a quantitative phylogenetic analysis. J Mol Evol. 2002;54:156–65.

    CAS  PubMed  Google Scholar 

  • Johnson PT, Ostfeld RS, Keesing F. Frontiers in research on biodiversity and disease. Ecol Lett. 2015;18:1119–33.

    PubMed  PubMed Central  Google Scholar 

  • Jones RAC. Plant virus emergence and evolution: origins, new encounter scenarios, factors driving emergence, effects of changing world conditions, and prospects for control. Virus Res. 2009;141:113–30.

    CAS  PubMed  Google Scholar 

  • Jridi C, Martin JF, Marie-Jeanne V, Labonne G, Blanc S. Distinct viral populations differentiate and evolve independently in a single perennial host plant. J Virol. 2006;80:2349–57.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Kay KM, Whittall JB, Hodges SA. A survey of nuclear ribosomal internal transcribed spacer substitution rates across angiosperms: an approximate molecular clock with life history effects. BMC Evol Biol. 2006;6:36.

    PubMed  PubMed Central  Google Scholar 

  • Keesing F, Holt RD, Ostfeld RS. Effects of species diversity on disease risk. Ecol Lett. 2006;9:485–98.

    CAS  PubMed  Google Scholar 

  • Keesing F, Belden LK, Daszk P, Dobson A, Harwell CD, Holt RD, Hudson P, Jolles A, Jones KE, Mitchell CE, Myers SS, Bogich T, Ostfeld RS. Impacts of biodiversity on the emergence and transmission of infectious diseases. Nature. 2010;468:647–52.

    CAS  PubMed  Google Scholar 

  • Kelly SE. Viral pathogens and the advantage of sex in the perennial grass Anthoxanthum odoratum: a review. Phil Trans R Soc Lond B. 1994;346:295–302.

    Google Scholar 

  • Kinoti WM, Constable FE, Nancarrow N, Plummer KM, Rodoni B. Analysis of intra-host genetic diversity of Prunus necrotic ringspot virus (PNRSV) using amplicon next generation sequencing. PLoS One. 2017;12:e0179284.

    PubMed  PubMed Central  Google Scholar 

  • Kreuze JF, Pérez A, Untiveros M, Quispe D, Fuentes S, Barker I, Simon R. Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: a generic method for diagnosis, discovery and sequencing of viruses. Virology. 2009;388:1–7.

    CAS  PubMed  Google Scholar 

  • Lanfear R, Kokko H, Eyre-Walker A. Population size and the rate of evolution. Trends Ecol Evol. 2014;29:33–41.

    PubMed  Google Scholar 

  • Lartey RT, Voss TC, Melcher U. Tobamovirus evolution: gene overlaps, recombination, and taxonomic implications. Mol Biol Evol. 1996;13:1327–38.

    CAS  PubMed  Google Scholar 

  • Lefeuvre P, Harkins GW, Lett J-M, Briddon RW, Chase MW, Moury B, Martin DP. Evolutionary time-scale of the begomoviruses: evidence from integrated sequences in the Nicotiana genome. PLoS One. 2011;6:e19193.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Levontin RC. The units of infection. Annu Rev Ecol Syst. 1970;1:1–18.

    Google Scholar 

  • Li H, Roossinck MJ. Genetic bottlenecks reduce population variation in an experimental RNA virus population. J Virol. 2004;78:10582–7.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lima ATM, Silva JCF, Silva FN, Castillo-Urquiza GP, Silva FF, Seah YM, Mizubuti ESG, Duffy S, Murilo Zerbini F. The diversification of begomovirus populations is predominantly driven by mutational dynamics. Virus Evol. 2017;3:vex005.

    PubMed  PubMed Central  Google Scholar 

  • Lipkin WI. The changing face of pathogen discovery and surveillance. Nat Rev Microbiol. 2013;11:133–41.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Little TJ, Shuker DM, Colegrave N, Day N, Graham AL. The coevolution of virulence: tolerance in perspective. PLoS Pathog. 2010;6:e1001006.

    PubMed  PubMed Central  Google Scholar 

  • Lively CM. The ecology of virulence. Ecol Lett. 2006;9:1089–95.

    PubMed  Google Scholar 

  • Malmstrom CM, Alexander HM. Effects of crop viruses on wild plants. Curr Op Virol. 2016;19:30–6.

    Google Scholar 

  • Malmstrom CM, Hughes CC, Newton LA, Stoner CJ. Virus infection in remnant native bunchgrasses from invaded California grasslands. New Phytol. 2005a;168:217–30.

    CAS  PubMed  Google Scholar 

  • Malmstrom CM, McCullough AJ, Johnson HA, Newton LA, Borer ET. Invasive annual grasses indirectly increase virus incidence in California native perennial bunchgrasses. Oecologia. 2005b;145:153–64.

    PubMed  Google Scholar 

  • Malmstrom CM, Shu R, Linton EW, Newton LA, Cook MA. Barley yellow dwarf viruses (BYDVs) preserved in herbarium specimens illuminate historical disease ecology of invasive and native grasses. J Ecol. 2007;95:1153–66.

    CAS  Google Scholar 

  • Malpica JM, Fraile A, Moreno I, Obies CI, Drake JW, García-Arenal F. The rate and character of spontaneous mutation in an RNA virus. Genetics. 2002;162:1505–11.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Malpica JM, Sacristán S, Fraile A, García-Arenal F. Association and host selectivity in multi-host pathogens. PLoS One. 2006;1:e41.

    PubMed  PubMed Central  Google Scholar 

  • Martín S, Elena SF. Application of game theory to the interaction between plant viruses during mixed infections. J Gen Virol. 2009;90:2815–20.

    PubMed  Google Scholar 

  • Maskell LC, Raybould AF, Cooper JI, Edwards ML, Gray AJ. Effects of turnip mosaic virus and turnip yellow mosaic virus on the survival, growth and reproduction of wild cabbage (Brassica oleracea). Ann Appl Biol. 1999;135:401–7.

    Google Scholar 

  • Massart S, Olmos A, Jijakli H, Candresse T. Current impact and future directions of high throughput sequencing in plant virus diagnostics. Virus Res. 2014;188:90–6.

    CAS  PubMed  Google Scholar 

  • Massart S, Candresse T, Gil J, Lacomme C, Predajna L, Ravnikar M, Reynard JS, Rumbou A, Saldarelli P, Škorić D, Vainio EJ, Valkonen JP, Vanderschuren H, Varveri C, Wetzel T. A framework for the evaluation of biosecurity, commercial, regulatory, and scientific impacts of plant viruses and viroids identified by NGS technologies. Front Microbiol. 2017;8:45.

    PubMed  PubMed Central  Google Scholar 

  • McKinney HH. Evidence of virus mutation in the common mosaic of tobacco. J Agric Res. 1935;51:951–81.

    Google Scholar 

  • McLeish MJ, Sacristán S, Fraille A, García-Arenal F. Scale dependencies and generalism in host use shape virus prevalence. Proc. R. Soc. B, 2017;284: 20172066.

    PubMed  Google Scholar 

  • Miyashita S, Kishino H. Estimation of the size of genetic bottlenecks in cell-to-cell movement of soil-borne wheat mosaic virus and the possible role of the bottlenecks in speeding up selection of variations in trans-acting genes or elements. J Virol. 2010;84:1828–37.

    CAS  PubMed  Google Scholar 

  • van Molken T, de Caluwe H, Hordijk CA, Leon-Reyes A, Snoeren TA, van Dam NM, Stuefer JF. Virus infection decreases the attractiveness of white clover plants for a non-vectoring herbivore. Oecologia. 2012;170:433–44.

    PubMed  PubMed Central  Google Scholar 

  • Monsion B, Froissart R, Michalakis Y, Blanc S. Large bottleneck size in Cauliflower mosaic virus populations during host plant colonization. PLoS Pathog. 2008;4:e1000174.

    PubMed  PubMed Central  Google Scholar 

  • Moreno A, De Blas C, Biurrun R, Nebreda M, Palacios I, Duque M, Fereres A. The incidence and distribution of viruses infecting lettuce, cultivated Brassica and associated natural vegetation in Spain. Ann Appl Biol. 2004;144:339–46.

    Google Scholar 

  • Morse SS, Schluederberg A. Emerging viruses: the evolution of viruses and viral diseases. J Infect Dis. 1990;162:1–7.

    CAS  PubMed  Google Scholar 

  • Moury B, Janzac B, Ruellan Y, Simon V, Ben Khalifa M, Fakhfakh H, Fabre F, Palloix A. Interaction patterns between Potato virus Y and eIF4E-mediated recessive resistance in the Solanaceae. J Virol. 2014;88:9799–807.

    PubMed  PubMed Central  Google Scholar 

  • Moury B, Fabre F, Hébrard E, Froissart R. Determinants of host species range in plant viruses. J Gen Virol. 2017;98:862–73.

    CAS  PubMed  Google Scholar 

  • Moya A, Rodríguez-Cerezo E, García-Arenal F. Genetic structure of natural populations of the plant RNA virus tobacco mild green mosaic virus. Mol Biol Evol. 1993;10:449–56.

    CAS  Google Scholar 

  • Moya A, Holmes EC, González-Candelas F. The population genetics and evolutionary epidemiology of RNA viruses. Annu Rev Microbiol. 2004;2:279–88.

    CAS  Google Scholar 

  • Nee S, Maynard-Smith J. The evolutionary biology of molecular parasites. Parasitology. 1990;100:S5–S18.

    PubMed  Google Scholar 

  • Ng TFF, Duffy S, Polston JE, Bixby E, Vallad GE, Breitbart M. Exploring the diversity of plant DNA viruses and their satellites using vector-enabled metagenomics on whiteflies. PLoS One. 2011;6:e19050.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Nieberding CM, Olivieri I. Parasites: proxies for host genealogy and ecology? Trends Ecol Evol. 2007;22:156–65.

    PubMed  Google Scholar 

  • Nsa IY, Kareem KT. Additive interactions of unrelated viruses in mixed infections of cowpea (Vigna unguiculata L. Walp). Front Plant Sci. 2015;6:812.

    PubMed  PubMed Central  Google Scholar 

  • Nuismer SL, Jordano P, Bascompte J. Coevolution and the architecture of mutualistic networks. Evolution. 2013;67:338–54.

    PubMed  Google Scholar 

  • Ostfeld RS, Keesing F. Effects of host diversity on infectious disease. Annu Rev Ecol Evol Syst. 2012;43:157–82.

    Google Scholar 

  • Ostfeld RS, Keesing F. Is biodiversity bad for your health? Ecosphere. 2017;8:e01676.

    Google Scholar 

  • Pagán I, Holmes EC. Long-term evolution of the Luteoviridae: time scale and mode of virus speciation. J Virol. 2010;84:6177–87.

    PubMed  PubMed Central  Google Scholar 

  • Pagán I, Alonso-Blanco C, García-Arenal F. The relationship of within-host multiplication and virulence in a plant-virus system. PLoS One. 2007;2:e786.

    PubMed  PubMed Central  Google Scholar 

  • Pagán I, Alonso-Blanco C, García-Arenal F. Host responses in life-history traits and tolerance to virus infection in Arabidopsis thaliana. PLoS Pathog. 2008;4:e1000124.

    PubMed  PubMed Central  Google Scholar 

  • Pagán I, Alonso-Blanco C, García-Arenal F. Differential tolerance to direct and indirect density-dependent costs of viral infection in Arabidopsis thaliana. PLoS Pathog. 2009;5:e1000531.

    PubMed  PubMed Central  Google Scholar 

  • Pagán I, Firth C, Holmes EC. Phylogenetic analysis reveals rapid evolutionary dynamics in the plant RNA virus genus Tobamovirus. J Mol Evol. 2010a;71:298–307.

    PubMed  Google Scholar 

  • Pagán I, Fraile A, Fernández-Fuello E, Montes N, Alonso-Blanco C, García-Arenal F. Arabidopsis thaliana as a model for plant-virus co-evolution. Philos Trans R Soc B. 2010b;365:1983–95.

    Google Scholar 

  • Pagán I, González-Jara P, Moreno-Letelier A, Rodelo-Urrego M, Fraile A, Piñero D, García-Arenal F. Effect of biodiversity changes in disease risk: exploring disease emergence in a plant-virus system. PLoS Pathog. 2012;8:e1002796.

    PubMed  PubMed Central  Google Scholar 

  • Pagán I, Montes N, Milgroom MG, García-Arenal F. Vertical transmission selects for reduced virulence in a plant virus and for increased resistance in the host. PLoS Pathog. 2014;10:e1004293.

    PubMed  PubMed Central  Google Scholar 

  • Pagán I, Fraile A, García-Arenal F. Evolution of the interactions of viruses with their plant hosts. In: Weaver SC, Denison M, Roossink MJ, Vignuzzi M, editors. Virus evolution: current research and future directions. Norfolk: Caister Academic Press; 2016. p. 127–54.

    Google Scholar 

  • Pinel-Galzi AS, Rakotomalala M, Sangu E, Sorho F, Kanyeka Z, Traoré O, Sérémé D, Poulicard N, Rabenantoandro Y, Sere Y, Konaté G, Ghesquiere A, Hébrard E, Fargette D. Theme and variations in the evolutionary pathways to virulence of an RNA plant virus species. PLoS Pathog. 2007;3:e180.

    PubMed  PubMed Central  Google Scholar 

  • Piry S, Wipf-Scheibel C, Martin J-F, Galan M, Berthier K. High throughput amplicon sequencing to assess within- and between-host genetic diversity in plant viruses. BioRXiv. 2017. https://doi.org/10.1101/168773.

  • Poulicard N, Pinel-Galzi A, Fargette D, Hébrard E. Alternative mutational pathways, outside the VPg, of rice yellow mottle virus to overcome eIF(iso)4G-mediated rice resistance under strong genetic constraints. J Gen Virol. 2014;95:219–24.

    CAS  PubMed  Google Scholar 

  • Power AG, Mitchell CE. Pathogen spillover in disease epidemics. Am Nat. 2004;164:S79–89.

    PubMed  Google Scholar 

  • Power AG, Borer ET, Hosseini P, Mitchell CE, Seabloom EW. The community ecology of barley/cereal yellow dwarf viruses in Western US grasslands. Virus Res. 2011;159:95–100.

    CAS  PubMed  Google Scholar 

  • Prendeville HR, Ye XH, Morris TJ, Pilson D. Virus infections in wild plant populations are both frequent and often unapparent. Am J Bot. 2012;99:1033–42.

    PubMed  Google Scholar 

  • Prendeville HR, Tenhumberg B, Pilson D. Effects of virus on plant fecundity and population dynamics. New Phytol. 2014;202:1346–56.

    PubMed  Google Scholar 

  • Pressing J, Reanney DC. Divided genomes and intrinsic noise. J Mol Evol. 1984;20:135–46.

    CAS  PubMed  Google Scholar 

  • Quenoiulle J, Vassilakos N, Moury B. Potato virus Y: a major crop pathogen that has provided major insights into the evolution of viral pathogenicity. Mol Plant Pathol. 2013;14:439–52.

    Google Scholar 

  • Randolph SE, Dobson DM. Pangloss revisited: a critique of the dilution effect and the biodiversity-buffers-disease paradigm. Parasitology. 2012;139:847–63.

    CAS  PubMed  Google Scholar 

  • Rato S, Golumbeanu M, Telenti A, Ciuffi A. Exploring viral infection using single-cell sequencing. Virus Res. 2016;239:55–68.

    PubMed  Google Scholar 

  • Rentería-Canett I, Xoconostle-Cázares B, Ruiz-Medrano R, Rivera-Bustamante RF. Geminivirus mixed infection on pepper plants: synergistic interaction between PHYVV and PepGMV. Virol J. 2011;8:104.

    PubMed  PubMed Central  Google Scholar 

  • Rochow WF. The role of mixed infections in the transmission of plant viruses by aphids. Annu Rev Phytopatol. 1972;10:101–24.

    Google Scholar 

  • Rodelo-Urrego M, Pagán I, González-Jara P, Betancourt M, Moreno-Letelier A, Ayllón MA, Fraile A, Piñero D, García-Arenal F. Landscape heterogeneity shapes host-parasite interactions and results in apparent plant-virus codivergence. Mol Ecol. 2013;22:2325–40.

    CAS  PubMed  Google Scholar 

  • Rodelo-Urrego M, García-Arenal F, Pagán I. The effect of ecosystem biodiversity on virus genetic diversity depends on virus species: a study of chiltepin-infecting begomoviruses in Mexico. Virus Evol. 2015;1:vev004.

    PubMed  PubMed Central  Google Scholar 

  • Rodríguez-Nevado C, Montes N, Pagán I. Ecological factors affecting the infection risk and population genetic diversity of a novel potyvirus in its native wild ecosystem. Front Plant Sci. 2017;8:1958.

    PubMed  PubMed Central  Google Scholar 

  • Roossinck MJ. Mechanisms of plant virus evolution. Annu Rev Phytopathol. 1997;35:191–209.

    CAS  PubMed  Google Scholar 

  • Roossinck MJ. Symbiosis versus competition in plant virus evolution. Nat Rev Microbiol. 2005;3:917–24.

    CAS  PubMed  Google Scholar 

  • Roossinck MJ. The big unknown: plant virus biodiversity. Curr Op Virol. 2011;1:63–7.

    Google Scholar 

  • Roossinck MJ. Plant virus metagenomics: biodiversity and ecology. Annu Rev Genet. 2012;46:357–67.

    Google Scholar 

  • Roossinck MJ. Deep sequencing for discovery and evolutionary analysis of plant viruses. Virus Res. 2017;239:82–6.

    CAS  PubMed  Google Scholar 

  • Roossinck MJ, Saha P, Wiley GB, Quan J, White JD, Lai H, Chavarría F, Shen G, Roe BA. Ecogenomics: using massively parallel pyrosequencing to understand virus ecology. Mol Ecol. 2010;19:81–8.

    PubMed  Google Scholar 

  • Roossinck MJ, Martin DP, Roumagnac P. Plant virus metagenomics: advances in virus discovery. Phytopatology. 2015;105:716–27.

    CAS  Google Scholar 

  • Sacristán S, García-Arenal F. The evolution of virulence and pathogenicity in plant pathogen populations. Mol Plant Pathol. 2008;9:369–84.

    PubMed  Google Scholar 

  • Sacristán S, Malpica JM, Fraile A, García-Arenal F. Estimation of population bottlenecks during systemic movement of tobacco mosaic virus in tobacco plants. J Virol. 2003;77:9906–11.

    PubMed  PubMed Central  Google Scholar 

  • Salvaudon L, De Moraes CM, Mescher MC. Outcomes of co-infection by two potyviruses: implications for the evolution of manipulative strategies. Proc R Soc Lon B. 2013;280:20122959.

    Google Scholar 

  • Sanjuán R, Agudelo-Romero P, Elena SF. Upper-limit mutation rate estimation for a plant RNA virus. Biol Lett. 2009;5:394–6.

    PubMed  PubMed Central  Google Scholar 

  • Sanjuán R, Nebot MR, Chirico N, Mansky LM, Belshaw R. Viral mutation rates. J Virol. 2010;84:9733–48.

    PubMed  PubMed Central  Google Scholar 

  • Sasu MA, Ferrari MJ, Du D, Winsor JA, Stephenson AG. Indirect costs of a nontarget pathogen mitigate the direct benefits of a virus-resistant transgene in wild Cucurbita. 2009;45:19067–71.

    Google Scholar 

  • Scholle SO, Ypma RJ, Lloyd AL, Koelle K. Viral substitution rate variation can Arise from the interplay between within-host and epidemiological dynamics. Am Nat. 2013;182:494–513.

    PubMed  Google Scholar 

  • Shuckla A, Pagán I, García-Arenal F. Effective tolerance based on resource reallocation is a virus-specific defence in Arabidopsis thaliana. Mol Plant Pathol. Published on line 30 Jan 2018.

    Google Scholar 

  • Sicard A, Yvon M, Timchenko T, Gronenborn B, Michalakis Y, Gutierrez S, Blanc S. Gene copy number is differentially regulated in a multipartite virus. Nat Commun. 2013;4:2248.

    PubMed  Google Scholar 

  • Sicard A, Michalakis Y, Gutierrez S, Blanc S. The strange lifestyle of multipartite viruses. PLoS Pathog. 2016;12:e1005819.

    PubMed  PubMed Central  Google Scholar 

  • Simmons HE, Holmes EC, Stephenson AG. Rapid evolutionary dynamics of zucchini yellow mosaic virus. J Gen Virol. 2008;89:1081–5.

    CAS  PubMed  Google Scholar 

  • Simmons HE, Dunham JP, Stack JC, Dickins BJA, Pagán I, Holmes EC, Stephenson AG. Deep sequencing reveals persistence of intra- and inter-host genetic diversity in natural and greenhouse populations of zucchini yellow mosaic virus. J Gen Virol. 2012;93:1831–40.

    CAS  PubMed  Google Scholar 

  • Simon AE, Bujarski JJ. RNA-RNA recombination and evolution in virus infected plants. Annu Rev Phytopathol. 1994;32:337–62.

    CAS  Google Scholar 

  • Stenger DC, Seifers DL, French R. Patterns of polymorphism in wheat streak mosaic virus: sequence space explored by a clade of closely related viral genotypes rivals that between the most divergent strains. Virology. 2002;302:58–70.

    CAS  PubMed  Google Scholar 

  • Stobbe AH, Roossinck MJ. Plant virus metagenomics: what we know and why we need to know more. Front Plant Sci. 2014;5:150.

    PubMed  PubMed Central  Google Scholar 

  • Stobbe AH, Melcherl U, Palmer MW, Roossinck MJ, Shen G. Co-divergence and host-switching in the evolution of tobamoviruses. J Gen Virol. 2012;93:408–18.

    PubMed  Google Scholar 

  • Stukenbrock EH, McDonald BA. The origin of plant pathogens in agro- ecosystems. Annu Rev Phytopathol. 2008;46:75–100.

    CAS  PubMed  Google Scholar 

  • Syller J. Facilitative and antagonistic interactions between plant viruses in mixed infections. Mol Plant Pathol. 2012;13:204–16.

    PubMed  Google Scholar 

  • Szathmáry E. Viral sex, levels of selection, and the origin of life. J Theor Biol. 1992;159:99–109.

    PubMed  Google Scholar 

  • Taiwo MA, Kareem KT, Nsa IY, Hughes JD’A. Cowpea viruses: effect of single and mixed infections on symptomatology and virus concentration. Virol J. 2007;4:95.

    PubMed  PubMed Central  Google Scholar 

  • Takahashi T, Sugawara T, Yamatsuta T, Isogai M, Natsuaki T, Yoshikawa N. Analysis of the spatial distribution or identical and two distinct virus populations differently labelled with cyan and yellow fluorescent proteins in coinfected plants. Phytopathology. 2007;97:1200–6.

    CAS  PubMed  Google Scholar 

  • Takeshita M, Shigemune N, Kikuhara K, Takanami Y. Spatial analysis for exclusive interactions between subgroups I and II of cucumber mosaic virus in cowpea. Virology. 2004;328:45–51.

    CAS  PubMed  Google Scholar 

  • Tepfer M. Risk assessment of virus-resistant transgenic plants. Annu Rev Phytopathol. 2002;40:467–91.

    CAS  PubMed  Google Scholar 

  • Thébaud G, Michalakis Y. Comment on “Large bottleneck size in Cauliflower mosaic virus populations during host plant colonization” by Monsion et al. (2008). PLoS Pathog. 2016;12:e1005512.

    PubMed  PubMed Central  Google Scholar 

  • Thompson AD. Interactions between plant viruses. I Appearance of new strains after mixed infection with Potato virus X strains. Virology. 1961;13:507–14.

    Google Scholar 

  • Thompson JN. The geographic mosaic of coevolution. Chicago: University of Chicago Press; 2005.

    Google Scholar 

  • Thresh JM. Cropping practices and virus spread. Annu Rev Phytopathol. 1982;20:193–218.

    Google Scholar 

  • Tomita R, Murai J, Miura Y, Ishikara H, Liu S, Kubotera Y, Honda A, Hatta R, Kuroda T, Hamada H, Sakamoto M, Munemura I, Nunomura O, Ishikawa K, Genda Y, Kawasaki S, Suzuki K, Meksem K, Kobayashi K. Fine mapping and DNA fiber FISH analysis locates the tobamovirus resistance gene L 3 of Capsicum chinense in a 400-kb region of R-like genes cluster embedded in highly repetitive sequences. Theor Appl Genet. 2008;117:1107–18.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tromas N, Elena SF. The rate and spectrum of spontaneous mutations in a plant RNA virus. Genetics. 2010;185:983–9.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tromas N, Zwart MP, Lafforgue G, Elena SF. Within-host spatiotemporal dynamics of plant virus infection at the cellular level. PLoS Genet. 2014a;10:e1004186.

    PubMed  PubMed Central  Google Scholar 

  • Tromas N, Zwart MP, Poulain M, Elena SF. Estimation of the in vivo recombination rate for a plant RNA virus. J Gen Virol. 2014b;95:724–32.

    CAS  PubMed  Google Scholar 

  • Trovão NS, Baele G, Vrancken B, Bielejec F, Suchard MA, Fargette D, Lemey P. Host ecology determines the dispersal patterns of a plant virus. Virus Evol. 2015;1:vev016.

    PubMed  PubMed Central  Google Scholar 

  • Tsuda S, Kirita M, Watanabe Y. Characterization of a pepper mild mottle tobamovirus strain capable of overcoming the L 3 gene-mediated resistance, distinct from the resistance-breaking Italian isolate. Mol Plant Microbe Interact. 1998;11:327–31.

    CAS  PubMed  Google Scholar 

  • Tugume AK, Mukasa SB, Valkonen JPT. Mixed infections of four viruses, the incidence and phylogenetic relationships of Sweet potato chlorotic fleck virus (Betaflexiviridae) isolates in wild species and sweetpotatoes in Uganda and evidence of distinct isolates in East Africa. PLoS One. 2016;11:e0167769.

    PubMed  PubMed Central  Google Scholar 

  • van der Walt E, Martin DP, Varsani A, Polston JE, Rybicki EP. Experimental observations of rapid maize streak virus evolution reveal a strand-specific nucleotide substitution bias. Virol J. 2008;5:104.

    PubMed  PubMed Central  Google Scholar 

  • Wang J, Moore NE, Deng Y-M, Eccles DA, Hall RJ. MinION nanopore sequencing of an influenza genome. Front Microbiol. 2017;6:766.

    Google Scholar 

  • Wanunu M. Nanopores: a journey towards DNA sequencing. Phys Life Rev. 2012;9:125–58.

    PubMed  PubMed Central  Google Scholar 

  • Woolhouse MEJ, Webster JP, Domingo E, Charlesworth B, Levin BR. Biological and biomedical implications of the co-evolution of pathogens and their hosts. Nat Genet. 2002;32:569–77.

    CAS  PubMed  Google Scholar 

  • Worobey M, Holmes EC. Evolutionary aspects of recombination in RNA viruses. J Gen Virol. 1999;80:2535–43.

    CAS  PubMed  Google Scholar 

  • Wu X, Xu Z, Shaw JG. Uncoating of tobacco mosaic virus RNA in protoplasts. Virology. 1994;200:256–62.

    CAS  PubMed  Google Scholar 

  • Wu B, Melcher U, Guo X, Wang X, Fan L, Zhou G. Assessment of codivergence of mastreviruses with their plant hosts. BMC Evol Biol. 2008;8:335.

    PubMed  PubMed Central  Google Scholar 

  • Wu B, Blanchard-Letort A, Liu Y, Zhou G, Wang X, Elena SF. Dynamics of molecular evolution and phylogeography of Barley yellow dwarf virus-PAV. PLoS One. 2011;6:e16896.

    CAS  PubMed  PubMed Central  Google Scholar 

  • Wu Q, Ding SW, Zhang Y, Zhu S. Identification of viruses and viroids by next-generation sequencing and homology-dependent and homology-independent algorithms. Annu Rev Phytopathol. 2015;53:425–44.

    CAS  PubMed  Google Scholar 

  • Wylie SJ, Li H, Dixon KW, Richards H, Jones MGK. Exotic and indigenous viruses infect wild populations and captive collections of temperate terrestrial orchids (Diuris species) in Australia. Virus Res. 2013;171:22–32.

    CAS  PubMed  Google Scholar 

  • Xu P, Chen F, Mannas JP, Feldman T, Sumner LW, Roossinck MJ. Virus infection improves drought tolerance. New Phytol. 2008;180:911–21.

    PubMed  Google Scholar 

  • Yasaka R, Nguyen HD, Ho SYW, Duchêne S, Korkmaz S, Nikolaos K, Takahashi H, Gibbs AJ, Ohshima K. The temporal evolution and global spread of Cauliflower mosaic virus, a plant pararetrovirus. PLoS One. 2014;9:e85641.

    PubMed  PubMed Central  Google Scholar 

  • Zwart MP, Willemsen A, Darós JA, Elena SF. Experimental evolution of pseudogenization and gene loss in a plant RNA virus. Mol Biol Evol. 2014;31:121–34.

    CAS  PubMed  Google Scholar 

Download references

Acknowledgment

IP was supported by grant (BIO2016-79165-R) and FGA was supported by grant (BFU2015-60418-R), both funded by Plan Nacional I + D + I, MINECO, Spain.

Author information

Authors and Affiliations

  1. Centro de Biotecnología y Genómica de Plantas UPM-INIA, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain

    Israel Pagán & Fernando García-Arenal

  2. E.T.S. Ingeniería Agronómica, Alimentaria y de Biosistemas, Madrid, Spain

    Israel Pagán & Fernando García-Arenal

Authors
  1. Israel Pagán
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Fernando García-Arenal
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Fernando García-Arenal .

Editor information

Editors and Affiliations

  1. Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA

    Martin F. Polz

  2. Faculty of Forestry and Environmental Management, University of New Brunswick, Fredericton, NB, Canada

    Om P. Rajora

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer International Publishing AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Pagán, I., García-Arenal, F. (2018). Population Genomics of Plant Viruses. In: Polz, M., Rajora, O. (eds) Population Genomics: Microorganisms. Population Genomics. Springer, Cham. https://doi.org/10.1007/13836_2018_15

Download citation

Publish with us

Policies and ethics

Search

Navigation