pan-Draft：从多个基因组自动重建物种代表性代谢模型

IF 10.1 1区生物学 Q1 BIOTECHNOLOGY & APPLIED MICROBIOLOGY

Genome Biology Pub Date : 2024-10-25 DOI:10.1186/s13059-024-03425-1

Nicola De Bernardini, Guido Zampieri, Stefano Campanaro, Johannes Zimmermann, Silvio Waschina, Laura Treu

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引用次数: 0

摘要

由于元基因组组装基因组（MAGs）具有典型的不完整和零散遗传信息，为不可培养物种准确重建基因组尺度代谢模型（GEMs）带来了挑战。现有工具利用单个基因组的序列同源性，而本研究则引入了泛草图（pan-Draft），这是一种基于泛反应组的方法，利用反复出现的遗传证据来确定物种级 GEM 的稳固核心结构。通过比较物种级的 MAGs 聚类，pan-Draft 解决了由于单个基因组的不完整性和污染所造成的问题，提供了高质量的草拟模型和辅助反应目录，为填补空白的步骤提供了支持。这种方法将提高我们对未培养物种代谢功能的理解。

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pan-Draft: automated reconstruction of species-representative metabolic models from multiple genomes

The accurate reconstruction of genome-scale metabolic models (GEMs) for unculturable species poses challenges due to the incomplete and fragmented genetic information typical of metagenome-assembled genomes (MAGs). While existing tools leverage sequence homology from single genomes, this study introduces pan-Draft, a pan-reactome-based approach exploiting recurrent genetic evidence to determine the solid core structure of species-level GEMs. By comparing MAGs clustered at the species-level, pan-Draft addresses the issues due to the incompleteness and contamination of individual genomes, providing high-quality draft models and an accessory reactions catalog supporting the gapfilling step. This approach will improve our comprehension of metabolic functions of uncultured species.

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来源期刊

Genome Biology Biochemistry, Genetics and Molecular Biology-Genetics

CiteScore

21.00

自引率

3.30%

发文量

241

审稿时长

2 months

期刊介绍： Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens. With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category. Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.