Pantagruel phylogenomic analysis of a bacterial pangenome covering 571 Rhizobiaceae genomes, with a focus on 41 Pseudorhizobium and Neorhizobium genomes

Comparative gebnomic analysis of 571 Rhizobiaceae genomes was conducted using the Pantagruel pipeline under the default settings as described by Lassalle et al. (2019). This pipeline is designed for the analysis of bacterial pangenomes, including the inference of a species tree, gene trees, and the detection of horizontal gene transfers (HGT) through species tree/gene tree reconciliations (Szöllősi et al. 2015). The whole set of information derived from the Pantagruel processing of the 571 Rhizobiaceae pangenome is stored into a SQLite 3 database. This includes:- metadata on the 571 organisms and their genome assemblies;- annotation of 3,370,771 coding sequences (CDSs);- their classification into 50,792 homologous gene families. In addition, for a subset of 41 genomes of strains of the genera Pseudorhizobium and Neorhizobium and their close relatives, a robust species tree and gene trees were reconstructed for 6,629 gene families represented in these genomes (covering 757,162 CDSs). For these gene families, species tree/gene tree reconciliation was used to infer evolutionary scenarios for each gene lineage, with events of gene duplication, origination, HGT and loss. This allowed the classification of genes into orthologous groups (i.e. a sub-clustering of the homologous 6,629 gene families). The database thus also hold information on:- 3,038,614 gene lineage events;- 19,016 orthologous groups.