Compressive pangenomics using mutation-annotated networks

Sumit Walia

doi:10.1038/s41588-025-02478-7

2026-01-12

PRE

Russell Corbett-Detig

Yatish Turakhia *

DOI：10.1038/s41588-025-02478-7

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摘要

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泛基因组学是一个新兴领域，它使用基因组集合而非单一参考基因组来减少偏差并捕获种内多样性。然而，现有的泛基因组数据格式在扩展到数百万个基因组时面临挑战，主要强调变异，常忽略底层突变事件和进化关系。本研究介绍了泛基因组突变注释网络（PanMAN），一种无损泛基因组表示方法，其文件大小压缩率相比现有保留变异的格式达到3.5–1,391×，性能在大型数据集上普遍提升。除压缩外，PanMAN通过编码跨基因组推断的详细突变和进化历史来增加表示能力，从而实现新的生物学见解。利用PanMAN，构建了一个包含8百万个公开序列的SARS-CoV-2泛基因组，仅需366 MB磁盘空间。我们还介绍了‘panmanUtils’工具包，支持常见分析并确保与现有软件的互操作性。PanMAN有望显著提升泛基因组分析的规模、速度、分辨率和范围。泛基因组突变注释网络（PanMAN）是一种编码微生物基因组间共享突变和进化历史的泛基因组数据结构，兼具高压缩率和增强的表示能力。

Keyword:

Pangenomics

Mutation-Annotated Network

Data Compression

Microbial Genomes

Evolutionary History

期刊

Nature Genetics

IF:

论文数:

737

被引数:

241

机构

university of california

学者数:

1.9W

论文数: 8.0K

被引数: 10

University of California San Diego

学者数:

4.6W

论文数: 3.5W

被引数: 924

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