Haplotype-resolved assembly of cultivated tetraploid potato

马铃薯是最重要的主食之一，是世界上产量最高的五大作物之一。全球每年马铃薯产量超过3500亿公斤，特别是在亚洲发展中国家，马铃薯产量呈上升趋势。但是，尽管具有这种社会和经济重要性，我们对现代马铃薯品种基因组组成的了解却微不足道，因为高度分化和同源四倍体基因组挑战了常用的基因组重测序方法。在这个项目中，我们建议使用我们新开发的组装方法来生成10个精心挑选的马铃薯的单倍型分解，染色体规模的组装。为此，我们选择了在现代马铃薯育种之初引进的品种，并在各种不同的育种计划中反复使用。因此，我们提出组装的40个单倍型在许多当代马铃薯品种中都是分离的，知道它们的序列可以支持对许多当代马铃薯的功能注释。为了展示这些新生成的单倍型如何在实践中实际使用，我们将40个单倍型组合到一个复杂的参考序列中（使用基于基因组图谱的比对算法），并使用它们对100多个公开可用的马铃薯基因组进行大规模的基因组多样性分析（用短读段测序）。这将使我们能够展示如何利用资源，同时解开现代马铃薯育种对基因组的影响。除了这些见解之外，组装的单倍型和如何利用它们的方法将成为马铃薯群落前所未有的工具，特别是支持基因组辅助育种的努力。

Potato is one of the most important staple foods and is among the five most produced crops in the world. Globally more than 350 billion kilograms of potato are produced per year with an increasing trend particularly in developing countries in Asia. But despite this social and economic importance, our knowledge of the genomic makeup modern potato cultivars is negligibly small as the highly divergent and autotetraploid genome challenges the commonly applied genome resequencing methods. In this project, we propose to use our newly developed assembly method to generate haplotype-resolved, chromosome-scale assemblies of ten carefully chosen potatoes. For this we have selected cultivars which were introduced in the beginning of modern potato breeding and were repeatedly used in various different breeding programs. The 40 haplotypes we propose to assemble are therefore segregating in many of the contemporary potato cultivars and knowing their sequence can support functional annotation of many of these contemporary potatoes. To show how these newly generated haplotypes can actually be used in practice, we will combine the 40 haplotypes assemblies to a complex reference sequence (using genome-graph based alignment algorithms) and use them for a broad-scale genomic diversity analysis of more than 100 publicly available potato genomes (sequenced with short reads). This will allow us to showcase how the resource can be used and at the same time untangle the genomic impact of modern potato breeding. Besides these insights, the assembled haplotypes and the means how to make use of them will be an unprecedented tool for the potato community and specifically support genomic-assisted breeding efforts.