Genomic structural variation in Nebbiolo grapevines at the individual, clonal and cultivar levels

Background: ‘Nebbiolo’ is a grapevine cultivar typical of north-western Italy, appreciated for producing high-quality red wines. Grapevine cultivars are characterized by possessing highly heterozygous genomes, including a great incidence of genomic rearrangements larger than 50 bp, so called structural variations (SVs). Even though abundant, SVs are an under-explored source of genetic variation mainly due to methodological limitations at their detection. Results: We employed a multiple platform approach to produce long-range genomic data for two diferent ‘Nebbiolo’ clones, namely: optical mapping, long-reads and linked-reads. We performed a haplotype-resolved de novo assembly for cultivar ‘Nebbiolo’ (clone CVT 71) and used an ab-initio strategy to annotate it. The annotated assembly enhanced our ability to detect SVs, enabling the study of genomic regions not present in the grapevines’ reference genome and accounting for their functional implications. We performed variant calling analyses at three diferent organizational levels: i) between haplotypes of clone CVT 71 (primary assembly vs haplotigs), ii) between ‘Nebbiolo’ and ‘Cabernet Sauvignon’ assemblies and iii) between clones CVT 71 and CVT 185, representing diferent ‘Nebbiolo’ biotypes. The cumulative size of non-redundant merged SVs indicated a total of 79.6 Mbp for the frst comparison and 136.1 Mbp for the second one, while no SVs were detected for the third comparison. Interestingly, SVs diferentiating cultivars and haplotypes afected similar numbers of coding genes. Conclusions: Our results suggest that SVs accumulation rate and their functional implications in ‘Nebbiolo’ genome are highly-dependent on the organizational level under study. SVs are abundant when comparing ‘Nebbiolo’ to a diferent cultivar or the two haplotypes of the same individual, while they turned absent between the two analysed