PanGraph: scalable bacterial pan-genome graph construction

Abstract

The genomic diversity of microbes is commonly parameterized as SNPs relative to a reference genome of a well-characterized, but arbitrary, isolate. However, any reference genome contains only a fraction of the microbial pangenome, the total set of genes observed in a given species. Reference-based approaches are thus blind to the dynamics of the accessory genome, as well as variation within gene order and copy number. With the widespread usage of long-read sequencing, the number of high-quality, complete genome assemblies has increased dramatically. In addition to pangenomic approaches that focus on the variation in the sets of genes present in different genomes, complete assemblies allow investigations of the evolution of genome structure and gene order. This latter problem, however, is computationally demanding with few tools available that shed light on these dynamics. Here, we present PanGraph, a Julia-based library and command line interface for aligning whole genomes into a graph. Each genome is represented as a path along vertices, which in turn encapsulate homologous multiple sequence alignments. The resultant data structure succinctly summarizes population-level nucleotide and structural polymorphisms and can be exported into several common formats for either downstream analysis or immediate visualization.

TheMycobacterium tuberculosiscomplex pangenome is small and driven by sub-lineage-specific regions of difference

“…To look at total pangenome content (both coding and non-coding), multiple whole genomes were aligned into a graph using Pangraph v0.7.2 (Noll et al, 2023). The DNA sequences from gene blocks present in at least one sub-lineage but completely absent in others were extracted.…”

Visualizing and quantifying structural diversity around mobile resistance genes

“…The pipeline then uses pangraph [ 9 ] to find homologous sequences. The pangraph algorithm was developed for whole genomes, and aims to identify stretches of homologous sequence within and across all input genomes, approximating multiple-genome alignment through iterative pairwise alignment of subsets of sequences with either minimap2 or mmseqs2.…”

“…Here, we aim to provide a starting point for quantitative analysis of structural diversity around mobile genes. We outline an annotation-free approach based on finding homologous sequence blocks with pangraph [ 9 ] that scales to thousands of sequences and connects visualization with quantification. As a demonstration, we apply our method to the flanking regions of 12 beta-lactamase genes.…”

Global genomic epidemiology ofblaGES-5carbapenemase-associated integrons

“…For the bla GES-5 flanking sequences, we generated a pangenome graph using PanGraph 47 (Figure S2 Next, we clustered the flanking sequences by their putative gene cassette contents. First, for the n=69/80 flanking sequences containing either an attI and at least one attC site, or at least two attC sites, we collated a list of PanGraph blocks found between the maximally upstream and downstream sites.…”