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Population Genomics: Microorganisms pp 233–265Cite as

Population Genomics of Plant Viruses

Part of the Population Genomics book series (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.

Keywords

  • Ecosystem biodiversity
  • Genomics of plant viruses
  • Multiplicity of infection
  • Plant virome assembly
  • Plant-virus coevolution
  • Time scale of plant virus evolution
  • Virus coinfection
  • Virus-virus interactions

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  • DOI: 10.1007/13836_2018_15
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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.

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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

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  1. Israel Pagán
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  2. Fernando García-Arenal
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Correspondence to Fernando García-Arenal .

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  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

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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

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