The genomic diversification of clonally propagated grapevines

Grapevine is a clonally propagated crop. Sixteen Zinfandel clones were acquired from Croatia, Italy, and California to study the nature and extent of somatic mutations that clones incur. To do this, a highly contiguous Zinfandel genome (Zin03) was sequenced, assembled, and annotated. Then, the clones were sequenced and compared to one another using Zin03 as a reference. Though most variants were heterozygous and shared among clones, confirming all but one's relationship to a single ancestral mother Zinfandel, unique SNPs, small insertions and deletions (INDELs), and structural variants that included transposable elements accrued in individual and subsets of clones. Overall, mutations tended to be more frequent in intergenic space than in genes, and heterozygous INDELs were more common in introns than exons. Relatively rare heterozygous variants in exons were increasingly deleterious alleles, though unique SNPs occurred most frequently in repetitive intergenic regions and INDELs were most prevalent in non-repetitive intergenic regions. A significantly larger percentage of CpG, CHG, and CHH sites in repetitive intergenic space experienced transition mutations than genic and non-repetitive intergenic spaces, and repetitive intergenic space had a significantly higher ratio of transitions to transversions than other regions of the genome. These results are consistent with the spontaneous deamination of methylated cytosines that are prevalent in repetitive intergenic space, inhibiting the transposition of mobile elements. These data support that intergenic space is a significant contributor to clonal genome diversification. In addition, these data support Muller's ratchet; clonal propagation is associated with the accumulation of deleterious mutations. In addition, these results support that some degree of selection against deleterious variants in coding regions may persist such that mutations are less frequent in coding than noncoding regions of the genome. Together, the results present interesting insights into the nature of mutations and genome diversification in a valuable, clonally propagated crop.