The paper itself goes into some more detail on that - the genetic diversity is found in the organization of the units among the chromosomes, while the units the

The paper itself goes into some more detail on that - the genetic diversity is found in the organization of the units among the chromosomes, while the units themselves (e.g. caffeine biosynthesis genes etc. are identical). This results in variations in gene expression levels, which alone is apparently enough to produce distinct varietals. > "While none of the different chromosomal aberrations we have identified is introducing new sequence variants, they are all capable of altering gene dosage between homoeologs and also total gene dosage in the case of aneuploidies, deletions and duplications. These changes in gene copy number may result in expression differences and this in turn may result in significant phenotypic variation, as shown by aneuploid somaclonal variants that frequently originate from tissue culture and somatic embryogenesis. The genomic rearrangements may therefore represent an important source of genetic diversity that is continuously replenishing the very limited nucleotide diversity available within the species." https://www.nature.com/articles/s41467-023-44449-8 https://www.nature.com/articles/s41467-023-44449-8 I suppose the takeaway is that using functional gene sequences alone (a common approach in the pre-whole-genome sequenceing era) to determine genetic similarity misses a lot of important information.