TY - JOUR

T1 - MetaPGN

T2 - a pipeline for construction and graphical visualization of annotated pangenome networks

AU - Peng, Ye

AU - Tang, Shanmei

AU - Wang, Dan

AU - Zhong, Huanzi

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

PY - 2018

Y1 - 2018

N2 - Pangenome analyses facilitate the interpretation of genetic diversity and evolutionary history of a taxon. However, there is 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.

AB - Pangenome analyses facilitate the interpretation of genetic diversity and evolutionary history of a taxon. However, there is 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.

UR - http://www.scopus.com/inward/record.url?scp=85057146860&partnerID=8YFLogxK

U2 - 10.1093/gigascience/giy121

DO - 10.1093/gigascience/giy121

M3 - Journal article

C2 - 30277499

AN - SCOPUS:85057146860

VL - 7

SP - 1

EP - 11

JO - GigaScience

JF - GigaScience

SN - 2047-217X

IS - 11

M1 - giy121

ER -