Population Genomics of Plant Viruses

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