pp 1-33 | Cite as

Population Genomics of Plant Viruses

  • Israel Pagán
  • Fernando García-Arenal
Part of the Population Genomics book series


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.


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 



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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© Springer International Publishing AG 2018

Authors and Affiliations

  1. 1.Centro de Biotecnología y Genómica de Plantas UPM-INIAUniversidad Politécnica de MadridPozuelo de Alarcón, MadridSpain
  2. 2.E.T.S. Ingeniería Agronómica, Alimentaria y de BiosistemasMadridSpain

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