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Abstract

Potato is the third most important food crop in the world. Despite its social and economic importance, the autotetraploid genome of cultivated potato has not been assembled yet. The distinct reconstruction all of four haplotypes remained an unsolved challenge. Here, we report the 3.1 Gb haplotype-resolved, chromosome-scale assembly of the autotetraploid potato cultivar, Otava. We assembled the genome with high-quality long reads coupled with single-cell sequencing of 717 pollen genomes and chromosome conformation capture data at a haplotyping precision of 99.6%. Unexpectedly, we found that almost 50% of the tetraploid genome were identical-by-descent with at least one of the other haplotypes. This high level of inbreeding contrasted with the extreme level of structural rearrangements encompassing nearly 20% of the genome. Overall, we annotated 148,577 gene models, where only 54% of the genes were present in all four haplotypes with an average of 3.2 copies per gene. Our work showcases how accurate assemblies of complex and partially inbred autotetraploid genomes can be generated. The newly established resource gives novel insights in the breeding history of autotetraploid potato and has the potential to change the future of genomics-assisted potato breeding.Competing Interest StatementThe authors have declared no competing interest.