Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.
Mathematisches Institut, Albert-Ludwigs University of Freiburg, 79104 Freiburg, Germany.
Nucleic Acids Res. 2018 Jan 9;46(1):e5. doi: 10.1093/nar/gkx977.
Horizontal transfer, gene loss, and duplication result in dynamic bacterial genomes shaped by a complex mixture of different modes of evolution. Closely related strains can differ in the presence or absence of many genes, and the total number of distinct genes found in a set of related isolates-the pan-genome-is often many times larger than the genome of individual isolates. We have developed a pipeline that efficiently identifies orthologous gene clusters in the pan-genome. This pipeline is coupled to a powerful yet easy-to-use web-based visualization for interactive exploration of the pan-genome. The visualization consists of connected components that allow rapid filtering and searching of genes and inspection of their evolutionary history. For each gene cluster, panX displays an alignment, a phylogenetic tree, maps mutations within that cluster to the branches of the tree and infers gain and loss of genes on the core-genome phylogeny. PanX is available at pangenome.de. Custom pan-genomes can be visualized either using a web server or by serving panX locally as a browser-based application.
水平转移、基因缺失和重复导致了细菌基因组的动态变化，其进化模式复杂多样。密切相关的菌株在许多基因的存在或缺失方面可能存在差异，而在一组相关分离物中发现的总共有多少个不同的基因——即泛基因组——通常比单个分离物的基因组大很多倍。我们开发了一种能够有效地识别泛基因组中直系同源基因簇的管道。该管道与一个强大而易于使用的基于网络的可视化工具相结合，用于交互式探索泛基因组。该可视化工具由连接组件组成，允许快速过滤和搜索基因，并检查它们的进化历史。对于每个基因簇，panX 都会显示一个比对、一个系统发育树、将该簇内的突变映射到树的分支，并推断核心基因组系统发育上基因的增益和损失。panX 可在 pangenome.de 上获得。可以使用 Web 服务器或通过在本地作为基于浏览器的应用程序提供 panX 来可视化自定义泛基因组。
