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Project #2889
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#2889 : Genome On Rails
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Name of Applicant : Eduardo Rocha
Date of application : 03-12-2015
Unit : Microbial Evolutionary Genomics
Location : François Jacob, 6ème étage
Phone : 0140613353
@ Mail : eduardo.rocha@pasteur.fr

Project context and summary :

Comparative genomics approaches in microbiology now use thousands of genomes to analyze a given species in different environmental or medical contexts. By collecting and comparing these genomic sequences, many  studies are focusing on  the overall gene content of a species (i.e. the pan-genome) to understand their evolution in terms of core and accessory parts. Variable regions are of primary importance to understand the adaptive potential of bacteria and contain genomic regions that are exchanged between strains by horizontal gene transfer (i.e. the mobilome). As recently suggested (Chan et al., Genome Biology 2015), a consensus representation of multiple genomes would provide a better analysis framework than using individual reference genomes. Here, we propose to extend this concept by giving it a formal mathematical representation using a graph model and by applying statistical methods to cluster gene families.


Related team publications :
Touchon M, Hoede C, Tenaillon O, Barbe V, Baeriswyl S, Bidet P, et al. Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet. 2009;5(1):e1000344.
Treangen, T. J. & Rocha EPC (2011) Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. PLoS Genet 7: e1001284.
Vallenet D, Belda E, Calteau A, Cruveiller S, Engelen S, Lajus A, Le Fèvre F, Longin C, Mornico D, Roche D, Rouy Z, Salvignol G, Scarpelli C, Thil Smith AA, Weiman M, Médigue C. MicroScope–an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data. Nucleic Acids Res., 2013, 41(Database issue):D636-47.
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Status : Declined


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