FROM ONE TO THE MANY GENOMES OF A PLANT: THE EVOLUTION OF THE GRAPEVINE PAN-GENOME

The analysis of variation in plants has revealed that their genomes are characterised by high levels of structural variation, consisting of both smaller insertion/deletions, mostly due to recent insertions of transposable elements, and of larger insertion/deletion similar to those termed in humans Copy Number Variants (CNVs). These observations indicate that a single genome sequence might not reflect the entire genomic complement of a species, and prompted us to introduce the concept of the plant pan-genome, including core genomic features common to all individuals and a Dispensable Genome (DG) composed of partially shared and/or non shared DNA sequence elements. The very active transposable element systems present in many plant genomes may account for a large fraction of the DG. The mechanisms by which the CNV-like variants are generated and the direction of the mutational events are still unknown. Uncovering the intriguing nature of the DG, i.e. its composition, origin and function, represents a step forward towards an understanding of the processes generating genetic diversity and phenotypic variation. Additionally, since the DG clearly appears to be for the most part the youngest and most dynamic component of the pan genome, it is of great interest to understand whether it is a major contributor to the creation of new genetic variation in plant evolution as well as in the artificial selection processes of plant breeding. We have resequenced to high coverage more than 50 grapevine accessions and used a variety of approaches to detect SNPs as well as structural variants of different size and origin, including de novo assembly of a selected set of genotypes. We will discuss the extent and composition of the pan genome in grapevine, the different mechanisms that generate and maintain the dispensable portion, the epigenetic and phenotypic effects of the DG and the rates and modes of creation of new genetic variation due to DG components.