Despite advances in sequencing technologies, assembly of complex plant genomes remains elusive due to polyploidy and high repeat content. Here we report PolyGembler for grouping and ordering contigs into pseudomolecules by genetic linkage analysis. Our approach also provides an accurate method with which to detect and fix assembly errors. Using simulated data, we demonstrate that our approach is of high accuracy and outperforms three existing state-of-the-art genetic mapping tools. Particularly, our approach is more robust to the presence of missing genotype data and genotyping errors. We used our method to construct pseudomolecules for allotetraploid lawn grass utilizing PacBio long reads in combination with restriction site-associated DNA sequencing, and for diploid Ipomoea trifida and autotetraploid potato utilizing contigs assembled from Illumina reads in combination with genotype data generated by single-nucleotide polymorphism arrays and genotyping by sequencing, respectively. We resolved 13 assembly errors for a published I. trifida genome assembly and anchored eight unplaced scaffolds in the published potato genome.

尽管测序技术取得了进步，但由于多倍体和高重复含量，复杂植物基因组的组装仍然难以实现。在这里，我们报告了 PolyGembler 通过遗传连锁分析将重叠群分组和排序为假分子。我们的方法还提供了一种准确的方法来检测和修复装配错误。使用模拟数据，我们证明我们的方法具有很高的准确性，并且优于三种现有的最先进的遗传作图工具。特别是，我们的方法对于缺失基因型数据和基因分型错误的存在更加稳健。我们使用我们的方法利用 PacBio 长读段结合限制性位点相关 DNA 测序构建异源四倍体草坪草的伪分子，并利用从Illumina 读段组装的重叠群并结合单核苷酸多态性生成的基因型数据构建二倍体三裂叶薯和同源四倍体马铃薯的伪分子分别通过阵列和测序进行基因分型。我们解决了已发表的I. trifida基因组组装的 13 个组装错误，并在已发表的马铃薯基因组中锚定了 8 个未放置的支架。