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Communication Dans Un Congrès Année : 2023

PANORAMA: comparative pangenomics tools to explore interspecies diversity of microbial genomes

Résumé

In recent years, to cope with the increase of genomes in databases, comparative genomics studies have focused on the overall gene content of a species, the pangenome, imposing a paradigm shift in the representation of knowledge and in the algorithms used. We developed PANORAMA, a flexible and open-source bioinformatics toolbox, which exploits multiprocessing, to perform rapid and easy-to-use comparative analysis of pangenomes using thousands of microbial genomes. It benefits from methods for the reconstruction and analysis of pangenome graphs, thanks to the PPanGGOLiN[1] software suite (https://github.com/labgem/PPanGGOLiN). PANORAMA integrates multiple features. It leverages homologous family conservation combined with graph connectivity to allow users to search for a specific genomic context in a set of pangenome graphs. Then, the presence-absence of the context in multiple pangenomes can be studied, and a completeness score is associated. PANORAMA also predicts biological systems, such as conjugation, secretion or defense systems, at the pangenome level. Pangenome gene families must be first associated with functional annotations using HMM profile searches. These HMMs are associated with a system-modeling describing gene presence/absence and synteny rules. PANORAMA detects genomic contexts corresponding to the models and verifies that presence/absence parameters fit with the associated rules. All generated results are associated to pangenome partitions, as well as to regions of genomic plasticity (RGPs), their spot of integration and their segmentation in conserved modules, thanks to panRGP[2] and panModule methods. The module associations can be used to find functional similarities between modules. A score of similarity between modules from different pangenomes is computed, corresponding to the number of common families compared to the total number of families in modules. PANORAMA aims to help microbiologists to understand the adaptive potential of bacteria and, with the exploration of functional modules in different species, to better understand the evolutionary dynamics behind the metabolic diversity of microorganisms. Future developments will integrate additional models for the annotation of KEGG modules or Polysaccharide Utilization Loci. We are also working on the integration of pangenomes in graph databases, such as Neo4J, to address the challenge of large-scale comparative pangenomics. Keywords: Pangenome graph, Bioinformatic software, Microbial Genomics, Comparative pangenomics, Biological systems References: 1) Gautreau, Guillaume, et al. "PPanGGOLiN: depicting microbial diversity via a partitioned pangenome graph." PLoS computational biology 16.3 (2020): e1007732. 2) Bazin, Adelme, et al. "panRGP: a pangenome-based method to predict genomic islands and explore their diversity." Bioinformatics 36.Supplement_2 (2020): i651-i658.
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Dates et versions

hal-04371302 , version 1 (03-01-2024)

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  • HAL Id : hal-04371302 , version 1

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Jérôme Arnoux, Jean Mainguy, Laura Bry, Quentin Fernandez De Grado, David Vallenet, et al.. PANORAMA: comparative pangenomics tools to explore interspecies diversity of microbial genomes. The local pangenome, Oct 2023, Alicante, Spain. ⟨hal-04371302⟩
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