We describe an integrative approach to improve contiguity and haploidy of a reference genome assembly and demonstrate its impact with practical examples. With two novel features of Lep-Anchor software and a combination of dense linkage maps, overlap detection and bridging long reads, we generated an improved assembly of the nine-spined stickleback (Pungitius pungitius) reference genome. We were able to remove a significant number of haplotypic contigs, detect more genetic variation and improve the contiguity of the genome, especially that of X chromosome. However, improved scaffolding cannot correct for mosaicism of erroneously assembled contigs, demonstrated by a de novo assembly of a 1.6-Mbp inversion. Qualitatively similar gains were obtained with the genome of three-spined stickleback (Gasterosteus aculeatus). Since the utility of genome-wide sequencing data in biological research depends heavily on the quality of the reference genome, the improved and fully automated approach described here should be helpful in refining reference genome assemblies.

中文翻译：

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使用 Lep-Anchor 软件自动改进刺鱼参考基因组组装

我们描述了一种提高参考基因组组装的连续性和单倍性的综合方法，并通过实际示例证明了其影响。借助Lep-Anchor软件的两个新功能以及密集连锁图、重叠检测和桥接长读的组合，我们生成了九刺棘鱼 ( Pungitius pungitius)的改进组件) 参考基因组。我们能够去除大量单倍型重叠群，检测更多遗传变异并改善基因组的连续性，尤其是 X 染色体的连续性。然而，改进的脚手架无法纠正错误组装的重叠群的镶嵌现象，1.6-Mbp 倒置的从头组装证明了这一点。三刺棘鱼 ( Gasterosteus aculeatus ) 的基因组获得了定性相似的收益。由于全基因组测序数据在生物学研究中的效用在很大程度上取决于参考基因组的质量，因此此处描述的改进和全自动方法应该有助于改进参考基因组组装。