[Paper Review] PanGeneHome : A Web Interface to Analyze Microbial Pangenomes

Camille Loiseau, Victor Hatte+17 more|arXiv (Cornell University)|May 15, 2018

Genomics and Phylogenetic Studies28 references3 citations

TL;DR

PanGeneHome is a web-based platform that enables researchers to analyze microbial pangenomes across 615 taxa, including 182 species and 49 orders, by providing gene conservation levels, pangenome and core-genome curves, dendrograms based on gene content and average amino acid identity (AAI), and functional annotations for core, accessory, and unique genes. The tool supports comparative analysis across any selected taxa, offering an integrated, user-friendly interface for pangenome exploration.

ABSTRACT

PanGeneHome is a web server dedicated to the analysis of available microbial pangenomes. For any prokaryotic taxon with at least three sequenced genomes, PanGeneHome provides (i) conservation level of genes, (ii) pangenome and core-genome curves, estimated pangenome size and other metrics, (iii) dendrograms based on gene content and average amino acid identity (AAI) for these genomes, and (iv) functional categories and metabolic pathways represented in the core, accessory and unique gene pools of the selected taxon. In addition, the results for these different analyses can be compared for any set of taxa. With the availability of 615 taxa, covering 182 species and 49 orders, PanGeneHome provides an easy way to get a glimpse on the pangenome of a microbial group of interest. The server and its documentation are available at http://pangenehome.lmge.uca.fr.

Motivation & Objective

• To provide a centralized, accessible web interface for microbial pangenome analysis across diverse prokaryotic taxa.
• To enable researchers to compare pangenome characteristics—including core and accessory gene pools—across multiple taxa simultaneously.
• To integrate functional annotation of genes in core, accessory, and unique gene pools to support biological interpretation.
• To estimate pangenome size and related metrics such as core-genome curves and gene conservation levels for any selected taxon with at least three sequenced genomes.

Proposed method

• The platform ingests genomic data from public databases for prokaryotic taxa with at least three sequenced genomes.
• It computes gene conservation levels by identifying orthologous gene clusters across genomes using sequence similarity and clustering algorithms.
• Pangenome and core-genome curves are generated by progressively adding genomes and tracking the cumulative number of unique and shared genes.
• Dendrograms are constructed using gene content similarity and average amino acid identity (AAI) to reflect evolutionary relationships.
• Functional categories and metabolic pathways are assigned to genes using databases such as COG and KEGG, and summarized for core, accessory, and unique gene pools.
• The system supports comparative analysis across user-selected taxa through a unified web interface with interactive visualization and exportable results.

Experimental results

Research questions

• RQ1 How does the pangenome size and core-genome size vary across different prokaryotic taxa with at least three sequenced genomes?
• RQ2 What is the distribution of functional categories and metabolic pathways in the core, accessory, and unique gene pools of a given microbial group?
• RQ3 How do gene content-based and AAI-based dendrograms compare in reflecting evolutionary relationships among closely related microbial strains?
• RQ4 To what extent can pangenome metrics such as gene conservation and curve trends predict genomic plasticity in microbial species?
• RQ5 How can comparative pangenome analysis across multiple taxa reveal patterns of gene gain, loss, and horizontal transfer?

Key findings

• PanGeneHome provides pangenome and core-genome curves for 615 taxa, including 182 species and 49 orders, enabling systematic pangenome trend analysis.
• The platform estimates pangenome size and gene conservation levels for each selected taxon, offering quantitative metrics for genomic diversity assessment.
• Dendrograms based on gene content and AAI are generated for each taxon, supporting phylogenetic and functional comparison.
• Functional annotation of core, accessory, and unique genes is available through COG and KEGG databases, revealing pathway enrichment in different gene pools.
• The system supports comparative analysis across any user-defined set of taxa, allowing side-by-side evaluation of pangenome characteristics.
• The web interface enables interactive exploration and export of results, enhancing accessibility for non-expert users in microbial genomics.