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Communication Dans Un Congrès Année : 2019

Comparative microbial pangenomics to explore mobilome dynamics

Résumé

Background: For the last decade, pangenomics has provided new tools for researchers to estimate genomic diversity by partitioning gene content in terms of “core” and “accessory” genome. However, the ”core genome” is highly related to the number of genomes included in a study limiting the relevance of comparisons between studies. Moreover, the concept of accessory genome lacks subtlety as it gathers genes with a large range of frequencies. Recently, a new tool named PPanGGOLiN was developed to exploit both gene neighborhood topology and gene frequency to classify gene families using a graph-based approach into a 3-class partitioning of ”persistent”, ”shell” and ”cloud” genome. Objectives: Using this new approach, we are establishing the pangenomes of all microbial species sufficiently represented in databanks. With such a resource, the variable regions of the pangenomes can be detected and split into modules. By studying module conservation between species, we can explore mobilome dynamics in a comparative pangenomics approach. Methods: Using the graph structure provided by PPanGGOLiN, modules are detected within each pangenome by integrating both co-occurrence and co-localization information. Then we search for conserved modules between species using network alignment methods. Results: The developed method can be applied on any species with a sufficient number of genomes. The collection of pangenomes with their predicted variable regions and modules will be made available to the research community. This resource may help to associate functional modules that are shared between species with common environmental factors or phenotypic traits.
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Dates et versions

hal-04359455 , version 1 (21-12-2023)

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  • HAL Id : hal-04359455 , version 1

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Adelme Bazin, Guillaume Gautreau, Claudine Médigue, Alexandra Calteau, David Vallenet. Comparative microbial pangenomics to explore mobilome dynamics. The 8th Congress of European Microbiologists, FEMS 2019, Jul 2019, Glasgow, United Kingdom. ⟨hal-04359455⟩
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