Pan Genome and Structural Variation Analysis using different Approaches for de novo Assembly and Haplotype Reconstruction

Structural variation plays an important role in the diversity of grape genomes. Here we show several approaches that allowed us to capture the pan-genome of different grape varieties, based on paired-end mapping and de novo assembly, each carrying its pros and cons. A dispensable genome, scattered across varieties, has been also found as a relevant hemizygous component. The low-coverage sequencing of four progeny individuals, derived from a self-pollinated “rkatsiteli” variety, allowed to resolve its two haplotypes at SNPs and SVs levels. Moreover, by leveraging nearly complete chromosome-level reconstruction of its genome via Hi-C contact matrix, it has been possible to determine syntelogs. This showed that, in many circumstances, the availability of a draft annotated genome can ensure a less biased representation of its actual gene content, accessing its functional dispensable genome and providing a better estimate of expression levels in RNA-Seq experiments.