Nebbiolo genome assembly allows surveying the occurrence and functional implications of genomic structural variations in grapevines (Vitis vinifera L.). Vitis vinifera

Nebbiolo is a grapevine (Vitis vinifera L.) cultivar typical of north-western Italy, appreciated for its use in producing high-quality red wines. Here, we assembled and annotated a genome for this cultivar to survey the occurrence of structural variations (SVs) and their genomic functional implications. SVs are a widely under-explored source of genetic variation due to methodological limitations and because they are generally associated to deleterious effects. In this work, we employed comparative approaches to detect the presence of SVs at different organizational levels in grapevines. Namely, between the two haplotypes of the same individual, between Nebbiolo clones representing two different biotypes and between different cultivars. At this aim, long-range genomic data was generated using multiple platforms, including long-reads, linked-reads and optical-mapping. Our results indicate that differential SVs occurring between Nebbiolo clones might be rare, while SVs are abundant when the two haplotypes of the same individual are compared. We also found that the highest number of SVs occurred when comparing different grapevine cultivars. Interestingly, SVs differentiating cultivars and haplotypes affected similar numbers of coding genes. In conclusion, we found that long-reads represent the most reliable genomic data for SVs detection, and that SVs accumulation rate and their functional implications in grapevine genomes is highly-dependent on the organizational level under study.