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Communication Dans Un Congrès Année : 2023

PPanGGOLiN V2: technical enhancement and new features to analyze thousands of prokaryotic genomes

Résumé

For 3 years, PPanGGOLiN[1] (https://github.com/labgem/PPanGGOLiN) has emerged as a solid and widespread solution to construct and analyze prokaryotic pangenome graphs. In contrast to other tools, it is based on a graphical and statistical model to enable efficient and stable partitioning of pangenomes in persistent, shell and cloud genomes. Moreover, using the pangenome graph, PPanGGOLiN is able to identify regions of genomic plasticity (RGPs), their spots of insertions and their segmentation in conserved modules, with the panRGP[2] and panModule methods. With the ever-increasing number of genomes available in databases, it is essential to optimize the execution and storage capacities of PPanGGOLiN. Here we present the second version of PPanGGOLiN with technical improvements and code revision leading to a more effective data compression of the pangenome file as well as a better user experience. A configuration file can be used for reproducible and tunable analyses. Also, new features have been added in order to enable novel analyses. First, we included a feature allowing to cluster the RGPs based on their family content to investigate the evolutionary dynamics of mobile genetic elements (MGE). Also, the pangenome information (partition, RGPs, spots, modules, …) can be projected on multiple new genomes without recomputing the full pangenome. Furthermore, a set of genes can be searched in the pangenome graph with the aim to extract their conserved genomic context. On top of this, metadata can be added to all pangenome elements and linked to PPanGGOLiN analyzes and outputs, such as functional annotation of gene families. The aim of this new version of PPanGGOLiN is to continue facilitating the study of the evolutionary dynamics of prokaryotic species in the era of high-throughput genomics, paving the way for comparative pangenomics. Keywords: Pangenome graph, Bioinformatic software, Microbial Genomics, Mobile genetic elements, 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-04371316 , version 1 (03-01-2024)

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  • HAL Id : hal-04371316 , version 1

Citer

Jean Mainguy, Jérôme Arnoux, Guillaume Gautreau, Adelme Bazin, David Vallenet, et al.. PPanGGOLiN V2: technical enhancement and new features to analyze thousands of prokaryotic genomes. The local pangenome, Oct 2023, Alicante, Spain. ⟨hal-04371316⟩
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