Genome assembly and functional characterization of three different clones of the Italian grapevine cultivar Nebbiolo.

Nebbiolo is a valuable Vitis vinifera cultivar from Piedmont, north-west Italy, and it is renowned for its use in producing high quality red wines. Very little information is available so far for this cultivar at molecular genetics or genomics level. In this work we present the assembly and the functional characterization of the genome of three clonal selections of the Nebbiolo variety. Genomic DNA libraries from Nebbiolo Michet (clone 71), Nebbiolo Picotener (clone 423) and Nebbiolo Lampia (clone 185) were deep sequenced using an Illumina HiSeq 1000 sequencer. A genomic coverage of 60x was achieved for all libraries. The three genomes were assembled using a bioinformatic pipeline which combines a reference-guided iterative mapping of the sequenced reads with a de novo assembly. Computational analysis showed differences ranging from 1.78 to 1.91 x 106 single nucleotide polymorphisms (SNPs) between the Nebbiolo clones and the Vitis vinifera PN40024 reference genome. Transposable elements, already found in genomes of other plants as well as of other V. vinifera, cover a fraction of more than 34% of the Nebbiolo genomes. A pool of RNA isolated from Nebbiolo plant organs at different developmental stages was deep sequenced and the obtained reads were used to re-annotate the three genomes. The results of this work will open a path for a better understanding of the Nebbiolo genetic variability and the interaction between environmental factors and genotype, along with the possible identification of molecular markers able to distinguish different 'Nebbiolo' clones. This research was funded by Fondazione Cassa di Risparmio di Cuneo, Project "NEBBIOLO GENOMICS: genomica strutturale e funzionale su aspetti patologici e qualitativi"