panRGP: a pangenome-based method to predict genomic islands and explore their diversity

Abstract

AbstractMotivationHorizontal gene transfer (HGT) is a major source of variability in prokaryotic genomes. Regions of Genome Plasticity (RGPs) are clusters of genes located in highly variable genomic regions. Most of them arise from HGT and correspond to Genomic Islands (GIs). The study of those regions at the species level has become increasingly difficult with the data deluge of genomes. To date no methods are available to identify GIs using hundreds of genomes to explore their diversity.ResultsWe present here the panRGP method that predicts RGPs using pangenome graphs made of all available genomes for a given species. It allows the study of thousands of genomes in order to access the diversity of RGPs and to predict spots of insertions. It gave the best predictions when benchmarked along other GI detection tools against a reference dataset. In addition, we illustrated its use on Metagenome Assembled Genomes (MAGs) by redefining the borders of the leuX tRNA hotspot, a well studied spot of insertion in Escherichia coli. panRPG is a scalable and reliable tool to predict GIs and spots making it an ideal approach for large comparative studies.AvailabilityThe methods presented in the current work are available through the following software: https://github.com/labgem/PPanGGOLiN. Detailed results and scripts to compute the benchmark metrics are available at https://github.com/axbazin/panrgp_supdata.Contactvallenet@genoscope.cns.fr and acalteau@genoscope.cns.frSupplementary informationNone.