A genome‐scale network reconstruction (GENRE) is a knowledgebase for an organism and has various applications. Available genome sequences have risen in recent years, but the number of curated GENREs has not kept pace. Existing yeast GENREs contain significant commission and omission errors. Current practices limit the quantity and quality of GENREs. An open and transparent phylogenomic‐driven framework is outlined to address these issues. The method is demonstrated with 33 yeasts and fungi in Dikarya. A pan‐fungal metabolic network called FYRMENT (Fungal and Yeast Metabolic Network) (https://github.com/LMSE/FYRMENT) is created, and annotated with ortholog groups from AYbRAH (https://github.com/LMSE/AYbRAH). Metabolic models for lower‐level taxons are compiled. The fungal pan‐GENRE contains 1553 orthologs, 2759 reactions, 2251 metabolites. The GENREs have higher genomic and metabolic coverage than existing yeast and fungal GENREs created with other methods. Metabolic simulations show the maximum amino acid yields from glucose differs between yeast lineages, indicating metabolic networks have evolved. Curating genomes and reactions at higher taxonomic‐levels increases the quantity and quality of GENREs than conventional approaches. This approach can scale to other branches in the tree of life.

中文翻译：

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泛基因组规模的网络重建：利用系统遗传学可以增加代谢模型的数量和质量。

基因组规模的网络重建（GENRE）是有机体的知识库，具有多种应用。近年来，可用的基因组序列有所增加，但是策划的GENRE的数量却没有跟上。现有的酵母GENRE包含重大的委托和遗漏错误。当前的做法限制了GENRE的数量和质量。为解决这些问题，概述了一个开放，透明的植物学驱动框架。用Dikarya中的33种酵母和真菌证明了该方法。创建了一个名为FYRMENT（真菌和酵母代谢网络）（https://github.com/LMSE/FYRMENT）的泛真菌代谢网络，并用AYbRAH（https://github.com/LMSE/AYbRAH）的直系同源物组进行注释。 ）。编译了较低级分类单元的代谢模型。真菌pan-GENRE包含1553个直系同源物，2759个反应，2251个代谢产物。与通过其他方法创建的现有酵母和真菌GENRE相比，GENRE具有更高的基因组和代谢覆盖率。代谢模拟显示，酵母谱系中葡萄糖的最大氨基酸产量不同，表明代谢网络已经进化。与常规方法相比，在更高的生物分类水平上进行基因组和反应的处理可提高GENRE的数量和质量。这种方法可以扩展到生命树中的其他分支。