Potato (Solanum tuberosum L.) is the most important tuber crop worldwide. Efforts are underway to transform the crop from a clonally propagated tetraploid into a seed-propagated, inbred-line-based hybrid, but this process requires a better understanding of potato genome. Here, we report the 1.67-Gb haplotype-resolved assembly of a diploid potato, RH89-039-16, using a combination of multiple sequencing strategies, including circular consensus sequencing. Comparison of the two haplotypes revealed ~2.1% intragenomic diversity, including 22,134 predicted deleterious mutations in 10,642 annotated genes. In 20,583 pairs of allelic genes, 16.6% and 30.8% exhibited differential expression and methylation between alleles, respectively. Deleterious mutations and differentially expressed alleles were dispersed throughout both haplotypes, complicating strategies to eradicate deleterious alleles or stack beneficial alleles via meiotic recombination. This study offers a holistic view of the genome organization of a clonally propagated diploid species and provides insights into technological evolution in resolving complex genomes.

马铃薯（ Solanum tuberosum L.）是世界上最重要的块茎作物。人们正在努力将作物从克隆繁殖的四倍体转化为种子繁殖的、基于近交系的杂交品种，但这一过程需要更好地了解马铃薯基因组。在这里，我们使用多种测序策略（包括循环一致性测序）的组合，报告了二倍体马铃薯 RH89-039-16 的 1.67-Gb 单倍型解析组装。两种单倍型的比较揭示了约 2.1% 的基因组内多样性，包括 10,642 个注释基因中的 22,134 个预测的有害突变。在20,583对等位基因中，分别有16.6%和30.8%表现出等位基因之间的差异表达和甲基化。有害突变和差异表达的等位基因分散在两种单倍型中，使根除有害等位基因或通过减数分裂重组堆叠有益等位基因的策略变得复杂。这项研究提供了克隆繁殖的二倍体物种的基因组组织的整体视图，并提供了对解决复杂基因组的技术进化的见解。