提出问题：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.

主要研究：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.

结果1-两套单倍型比较：Comparison of the two haplotypes revealed ~2.1% intragenomic diversity, including 22,134 predicted deleterious mutations in 10,642 annotated genes.

结果2-等位基因比较：In 20,583 pairs of allelic genes, 16.6% and 30.8% exhibited differential expression and methylation between alleles, respectively. 

结果3-有害突变分布特征：Deleterious mutations and differentially expressed alleles were dispersed throughout both haplotypes, complicating strategies to eradicate deleterious alleles or stack beneficial alleles via meiotic recombination.

结论：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.

马铃薯是全球最重要的块茎作物。目前育种学家们正在努力把马铃薯的育种从无性系繁殖的四倍体转变为种子繁殖的自交系杂种，但该过程需要我们对马铃薯的基因组具有深刻的了解。本文中，作者结合CCS测序手段在内的多种测序策略，报道了二倍体马铃薯RH89-039-16单倍型级别的组装结果，基因组大小为1.67 Gb。比较两个单倍型，作者发现单倍型基因组间的多样性约为2.1%，包括10642个基因上、22134个有害的突变。在20583个成对的等位基因中，16.6%的等位基因存在差异表达，而30.8%的等位基因存在甲基化水平的差异。有害突变和差异表达等位基因散状分布在整个单倍型上，使得通过减数分裂重组来消除有害基因或是固定有益位点变得尤其复杂。本文的研究为以无性系繁殖的二倍体物种基因组提供了一个参考视角，并为将来复杂基因组的解析提供了技术上的见解。

p.s. circular consensus sequencing（CCS）测序技术：在线性DNA分子的两端连接发夹接头（hairpin adapters），与接头结合的聚合酶可从接头移动，酶的读长一般大于插入片段长度，因此酶会绕着模板进行滚环测序，通过对同一区域多次测序，降低三代测序错误率高的难题，从而在保证测序长度的前提下，提高测序的准确性，获得高保真度的HiFi长reads。（Wenger et al., 2019, NBT, doi: 10.1038/s41587-019-0217-9）