Potato (Solanum tuberosum) is the most consumed non-cereal food crop. Most commercial potato cultivars are autotetraploids with highly heterozygous genomes, severely hampering genetic analyses and improvement. By leveraging the state-of-the-art sequencing technologies and polyploid graph binning, we achieved a chromosome-scale, haplotype-resolved genome assembly of a cultivated potato, Cooperation-88 (C88). Intra-haplotype comparative analyses revealed extensive sequence and expression differences in this tetraploid genome. We identified haplotype-specific pericentromeres on chromosomes, suggesting a distinct evolutionary trajectory of potato homologous centromeres. Furthermore, we detected double reduction events that are unevenly distributed on haplotypes in 1021 of 1034 selfing progeny, a feature of autopolyploid inheritance. By distinguishing maternal and paternal haplotype sets in C88, we simulated the origin of heterosis in cultivated tetraploid with a survey of 3110 tetra-allelic loci with deleterious mutations, which were masked in the heterozygous condition by two parents. This study provides insights into the genomic architecture of autopolyploids and will guide their breeding.

马铃薯（Solanum tuberosum）是消费最多的非谷类粮食作物。大多数商业马铃薯品种是同源四倍体，具有高度杂合的基因组，严重阻碍了遗传分析和改良。通过利用最先进的测序技术和多倍体图分箱，我们实现了栽培马铃薯Cooperative-88（C88）的染色体规模、单倍型解析的基因组组装。单倍型内比较分析揭示了该四倍体基因组中广泛的序列和表达差异。我们在染色体上鉴定出了单倍型特异性的着丝粒周围，这表明马铃薯同源着丝粒的独特进化轨迹。此外，我们在 1034 个自交后代中的 1021 个中检测到单倍型分布不均匀的双还原事件，这是同源多倍体遗传的一个特征。通过区分 C88 中的母本和父本单倍型集，我们通过调查 3110 个具有有害突变的四等位基因位点来模拟栽培四倍体中杂种优势的起源，这些突变在杂合条件下被两个亲本掩盖。这项研究提供了对同源多倍体基因组结构的见解，并将指导其育种。