Genome-scale computational approaches are opening opportunities to model and predict favorable combination of traits for strain development. However, mining the genome of complex hybrids is not currently an easy task, due to the high level of redundancy and presence of homologous. For example, Saccharomyces pastorianus is an allopolyploid sterile yeast hybrid used in brewing to produce lager-style beers. The development of new yeast strains with valuable industrial traits such as improved maltose utilization or balanced flavor profiles are now a major ambition and challenge in craft brewing and distilling industries. Moreover, no genome annotation for most of these industrial strains have been published. Here, we developed HybridMine, a new user-friendly, open-source tool for functional annotation of hybrid aneuploid genomes of any species by predicting parental alleles including paralogs. Our benchmark studies showed that HybridMine produced biologically accurate results for hybrid genomes compared to other well-established software. As proof of principle, we carried out a comprehensive structural and functional annotation of complex yeast hybrids to enable system biology prediction studies. HybridMine is developed in Python, Perl, and Bash programming languages and is available in GitHub.

中文翻译：

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HybridMine：杂种基因组中等位基因遗传和基因拷贝数预测的管道及其在工业酵母中的应用

基因组规模的计算方法为建模和预测有利于性状发展的性状组合提供了机会。然而，由于高水平的冗余度和同源性的存在，挖掘复杂杂种的基因组目前不是一件容易的事。例如，酿酒酵母是一种异源多倍体无菌酵母杂种，用于酿造啤酒。具有有价值的工业特性（例如改善的麦芽糖利用或平衡的风味特征）的新型酵母菌株的开发现在是手工艺酿造和蒸馏行业的主要目标和挑战。此外，尚未公开大多数这些工业菌株的基因组注释。在这里，我们开发了HybridMine，这是一种新的用户友好型开源工具，可通过预测包括等位基因在内的亲本等位基因，对任何物种的杂交非整倍体基因组进行功能注释。我们的基准研究表明，与其他完善的软件相比，HybridMine对杂交基因组产生了生物学上准确的结果。作为原理证明，我们对复杂的酵母杂种进行了全面的结构和功能注释，以进行系统生物学预测研究。HybridMine是使用Python，Perl和Bash编程语言开发的，可在GitHub中使用。