Structural Variation and Genome Complexity: Is Dispensable Really Dispensable?

Genome data obtained from different plant species show how plastic, variable and complex plant genomes are. In particular, the presence of high levels of structural variation (i.e. insertion/deletion polymorphisms that are larger than 1 Kb) prompted us to extend to plant species the concept of pan-genome, which had been originally proposed for bacteria. The pan genome is composed of a core portion, present in all the individuals, and a dispensable portion, not present in all the individuals. The advent of next-generation sequencing (NGS) opened the possibility of re-sequencing the whole genome of several subjects. This led researchers to realize the need of deeply characterizing the genomes of plant species at a population level, since a single genome sequence is not adequate to represent all cultivars and/or populations. Population-scale whole genome resequencing efforts are being performed with the aim of investigating the pan-genome of different plant species. Such efforts will produce catalogues of structural variants (SVs), ultimately defining a species dispensable genome. Here we will discuss methods available for the detection of SVs, with special emphasis on the latest methodological developments. We will then emphasize the importance of SVs (and hence dispensable genome) for plant evolution, their possible functional roles and their importance for understanding the genetic bases of phenotypic variation and adaptation to stress