MetaPGN: a pipeline for construction and graphical visualization of annotated pangenome networks

Ye Peng; Shanmei Tang; Dan Wang; Huanzi Zhong; Huijue Jia; Xianghang Cai; Zhaoxi Zhang; Minfeng Xiao; Huanming Yang; Jian Wang; Karsten Kristiansen; Xun Xu; Junhua Li

doi:10.1093/gigascience/giy121

MetaPGN: a pipeline for construction and graphical visualization of annotated pangenome networks

Ye Peng, Shanmei Tang, Dan Wang, Huanzi Zhong, Huijue Jia, Xianghang Cai, Zhaoxi Zhang, Minfeng Xiao, Huanming Yang, Jian Wang, Karsten Kristiansen, Xun Xu, Junhua Li

Genome Research and Molecular Bio Medicine

6 Citations (Scopus)

52 Downloads (Pure)

Abstract

an urgent and unmet need to develop new tools for advanced pangenome construction and visualization, especially for metagenomic data. Here, we present an integrated pipeline, named MetaPGN, for construction and graphical visualization of pangenome networks from either microbial genomes or metagenomes. Given either isolated genomes or metagenomic assemblies coupled with a reference genome of the targeted taxon, MetaPGN generates a pangenome in a topological network, consisting of genes (nodes) and gene-gene genomic adjacencies (edges) of which biological information can be easily updated and retrieved. MetaPGN also includes a self-developed Cytoscape plugin for layout of and interaction with the resulting pangenome network, providing an intuitive and interactive interface for full exploration of genetic diversity. We demonstrate the utility of MetaPGN by constructing Escherichia coli pangenome networks from five E. coli pathogenic strains and 760 human gut microbiomes,revealing extensive genetic diversity of E. coli within both isolates and gut microbial populations. With the ability to extract and visualize gene contents and gene-gene physical adjacencies of a specific taxon from large-scale metagenomic data, MetaPGN provides advantages in expanding pangenome analysis to uncultured microbial taxa.

Original language	English
Article number	giy121
Journal	GigaScience
Volume	7
Issue number	11
Pages (from-to)	1-11
ISSN	2047-217X
DOIs	https://doi.org/10.1093/gigascience/giy121
Publication status	Published - 2 Oct 2018

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10.1093/gigascience/giy121Licence: CC BY

MetaPGNFinal published version, 655 KBLicence: CC BY

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title = "MetaPGN: a pipeline for construction and graphical visualization of annotated pangenome networks",

abstract = "an urgent and unmet need to develop new tools for advanced pangenome construction and visualization, especially for metagenomic data. Here, we present an integrated pipeline, named MetaPGN, for construction and graphical visualization of pangenome networks from either microbial genomes or metagenomes. Given either isolated genomes or metagenomic assemblies coupled with a reference genome of the targeted taxon, MetaPGN generates a pangenome in a topological network, consisting of genes (nodes) and gene-gene genomic adjacencies (edges) of which biological information can be easily updated and retrieved. MetaPGN also includes a self-developed Cytoscape plugin for layout of and interaction with the resulting pangenome network, providing an intuitive and interactive interface for full exploration of genetic diversity. We demonstrate the utility of MetaPGN by constructing Escherichia coli pangenome networks from five E. coli pathogenic strains and 760 human gut microbiomes,revealing extensive genetic diversity of E. coli within both isolates and gut microbial populations. With the ability to extract and visualize gene contents and gene-gene physical adjacencies of a specific taxon from large-scale metagenomic data, MetaPGN provides advantages in expanding pangenome analysis to uncultured microbial taxa.",

author = "Ye Peng and Shanmei Tang and Dan Wang and Huanzi Zhong and Huijue Jia and Xianghang Cai and Zhaoxi Zhang and Minfeng Xiao and Huanming Yang and Jian Wang and Karsten Kristiansen and Xun Xu and Junhua Li",

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AU - Peng, Ye

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AU - Jia, Huijue

AU - Cai, Xianghang

AU - Zhang, Zhaoxi

AU - Xiao, Minfeng

AU - Yang, Huanming

AU - Wang, Jian

AU - Kristiansen, Karsten

AU - Xu, Xun

AU - Li, Junhua

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AB - an urgent and unmet need to develop new tools for advanced pangenome construction and visualization, especially for metagenomic data. Here, we present an integrated pipeline, named MetaPGN, for construction and graphical visualization of pangenome networks from either microbial genomes or metagenomes. Given either isolated genomes or metagenomic assemblies coupled with a reference genome of the targeted taxon, MetaPGN generates a pangenome in a topological network, consisting of genes (nodes) and gene-gene genomic adjacencies (edges) of which biological information can be easily updated and retrieved. MetaPGN also includes a self-developed Cytoscape plugin for layout of and interaction with the resulting pangenome network, providing an intuitive and interactive interface for full exploration of genetic diversity. We demonstrate the utility of MetaPGN by constructing Escherichia coli pangenome networks from five E. coli pathogenic strains and 760 human gut microbiomes,revealing extensive genetic diversity of E. coli within both isolates and gut microbial populations. With the ability to extract and visualize gene contents and gene-gene physical adjacencies of a specific taxon from large-scale metagenomic data, MetaPGN provides advantages in expanding pangenome analysis to uncultured microbial taxa.

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MetaPGN: a pipeline for construction and graphical visualization of annotated pangenome networks

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