A dual genomic-epigenomic map of clonal evolution of 23 Pinot noir clones

Grapevine has been clonally propagated for millennia, accumulating somatic mutations and epigenetic modifications that create intra-varietal diversity. Previous studies using short-reads have been unable to resolve the full spectrum of this variation, particularly large structural variants and base modifications. Here, we generated a high-quality, phased diploid reference genome for the elite cultivar Pinot noir and performed Nanopore sequencing on 23 distinct clones. This enabled the creation of the first integrated map of clonal genetic and epigenetic variation in Vitis vinifera. Our assembly reveals a deep history of ancient inbreeding, with approximately 12% of the Pinot genome existing in extended Runs of Homozygosity. Downstream analysis reveals contrasting evolutionary dynamics across the molecular layers. Genetic variants (67,277 SNPs and 4,037 SVs) are mostly rare and shaped by strong purifying selection, evidenced by their depletion from coding regions. A substantial fraction of the structural variation among clones is mechanistically linked to instability in repetitive DNA, particularly centromeric repeats. In contrast, epigenetic variants in the CG context (250,382 DMCs) are abundant and significantly enriched within gene bodies, suggesting they are a major source of clonal divergence. Crucially, we demonstrate that the clonal phylogeny can be reconstructed with high fidelity using only CG methylation patterns, mirroring the structure derived from SNPs. This congruence, absent in transient non-CG methylation, suggest that stable CG epialleles are mitotically inherited, creating a persistent epigenetic signature of clonal ancestry that fundamentally shapes grapevine identity.