Pangenome analysis of Xanthomonas oryzae using PanExplorer application

In the past decade, the pan-genome concept has been largely employed to investigate the bacterial comparative genomics and evolution analyses. Many programs have been developed for this purpose but a need is still present for the exploration and visualization of data derived from pan-genome analyses. To address this question, we developed a webbased application, PanExplorer, which will perform pan-genome analysis based on various pangenome reconstruction tools and expose resulting information as a comprehensive and easy way, through several modules facilitating the exploration of gene clusters and interpretation of data. The application allows interactive data exploration at different levels: Pan-genome visualization as a presence/absence heatmap. This overview allows to easily identify and distinguish core-genes (present in all strains), cloud genes (genes from the accessory genome) and genome-specific genes. Physical map of core-genes and strain-specific genes can be displayed as a circular genomic representation (Circos), for each genome taken independently. Synteny analysis. The conservation of gene order between genomes can be investigated using graphical representations Visual inspection of a specific cluster. The application guarantees an up-to-date availability of public genomes, to be analyzed onthe-fly, and represents a versatile tool for genome exploration filling a need for bacteriologist community. Among perspectives and further development, new functionalities might be implemented shortly such as on-line pan-genome wide association studies (panGWAS) based on Scoary software or COG enrichment statistical studies. PanExplorer relies on several Javascript libraries for visualization and is freely available at http://panexplorer.southgreen.fr. Using this application applied to all the Xanthomonas oryzae genomes available at NCBI combined with our own strains collected in the field by the team, we aim to explore the pangenome within the Xanthomonas oryzae species for the discovery of new pathovarspecific genes or the identification of genomic signatures of emerging strains.