Microbial evolutionary genomics

Questions

Our scientific activities are centered on the bioinformatics and biostatistics analysis of genomes, at the crossroads of molecular evolution, population genetics, evolutionary ecology and molecular genetics. We focus on four major questions: 1) How and why are genomes organized? 2) How are such organizational features evolving in face of the extensive genome dynamics? 3) What are the roles of mobile elements in the trade-offs between organization and dynamics? 4) What is the interplay between genome dynamics and bacterial pathogen emergence at the microevolutionary and epidemiological scale?

Software

  • Swelfe, identification of degenerate repeats in genes, proteins and 3D structures.
  • Repseek, identification of degenerate repeats in genomes.
  • Repeatoire, ab inito prediction of repeat families.
  • GrowthPred, prediction of growth-related traits in microbes from genomic and metagenomic data.
  • T3SSscan- FLAGscan, prediction of protein secretion systems in diderms (prokaryotes).
  • Cassys, search for relaxases and key components of type IV secretion systems in proteomes using an HMM profiles database

Databases

Some recent publications

  • Rocha EP. (2013) Evolution. With a little help from prokaryotes. Science. 339(6124):1154-5.
  • Brisse S, Passet V, Haugaard AB, Babosan A, Kassis-Chikhani N, Struve C, Decré D. (2013) wzi gene sequencing, a rapid method to determine the capsular type of Klebsiella strains. J Clin Microbiol.
  • Bobay LM, Touchon M, Rocha EP. (2013) Manipulating or superseding host recombination functions: a dilemma that shapes phage evolvability. PLoS Genet. 9(9):e1003825. [FULL TEXT]
  • Cantinelli T, Chenal-Francisque V, Diancourt L, Frezal L, Leclercq A, Wirth T, Lecuit M, Brisse S. (2013) "Epidemic Clones" of Listeria monocytogenes Are Widespread and Ancient Clonal Groups. J Clin Microbiol. 51(11):3770-9.
  • Zhou Z, McCann A, Litrup E, Murphy R, Cormican M, Fanning S, Brown D, Guttman DS, Brisse S, Achtman M. (2013) Neutral genomic microevolution of a recently emerged pathogen, Salmonella enterica serovar Agona. PLoS Genet. 9(4):e1003471. [FULL TEXT]
  • Nogueira T, Touchon M, Rocha EP. (2012) Rapid evolution of the sequences and gene repertoires of secreted proteins in bacteria. PLoS One. 7(11):e49403. [FULL TEXT]
  • Abby SS, Rocha EPC (2012) The Non-Flagellar Type III Secretion System Evolved from the Bacterial Flagellum and Diversified into Host-Cell Adapted Systems. PLoS Genet 8:e1002983.  [FULL TEXT]
  • Guglielmini J, de la Cruz F, Rocha EPC (2012) Evolution of Conjugation and Type IV Secretion Systems. Mol Biol Evol in advanced press. [FULL TEXT]
  • Namouchi A, Didelot X, Schock U, Gicquel B, Rocha EPC (2012) After the bottleneck: genome wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination and natural selection. Genome Research 22:721-34.
  • Gama JA, Abby SS, Vieira-Silva S, Dionisio F, Rocha EPC (2012) Immune subversion and quorum-sensing shape the variation in infectious dose among bacterial pathogens. Plos Pathogens 8: e1002503. [FULL TEXT] 
  • Vieira-Silva S, Touchon M, Abby S, Rocha EPC (2011) Investment in rapid growth shapes the evolutionary rates of essential proteins. Proc Natl Acad Sci USA 108:20030-20035.  [FULL TEXT]
  • Guglielmini J, Quintais L, Garcillán-Barcia MP, de la Cruz F, Rocha EPC (2011) The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation. PLoS Genet 7:e1002222. [FULL TEXT]
  • WarneckeT, Rocha EPC (2011) Function-specific accelerations in rates of sequence evolution suggest predictable epistatic responses to reduced effective population size. Mol Biol Evol 28:2339-49. [FULL TEXT]
  • Treangen TJ & Rocha EPC (2011) Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes. PLoS Genet 7: e1001284. [FULL TEXT]
  • Smillie C, Garcillán-Barcia MP, Francia MV, Rocha EPC, de la Cruz F (2010) The mobility of plasmids. Microbiol Mol Biol Rev. 74:434-52. [FULL TEXT]
  • Touchon M, Rocha EPC (2010) The small, slow and specialized CRISPR and anti-CRISPR of Escherichia and Salmonella. PLoS One 5:e11126. [FULL TEXT]
  • Vieira-Silva S, Touchon M, Rocha EPC (2010) No evidence for elemental-based streamlining of prokaryotic genomes. Trends Ecol Evol 25:319-20. [FULL TEXT]
  • Vieira-Silva S, Rocha EPC (2010) The Systemic Imprint of Growth Rates and its Uses in Ecological (Meta)genomics. PLoS Genetics 6:e1000808.[FULL TEXT]
  • Nogueira T, Rankin DJ, Touchon M, Taddei F, Brown SP, Rocha EPC (2009) Horizontal Gene Transfer of the Secretome Drives the Evolution of Bacterial Cooperation and Virulence. Curr Biol 19:1683-91. [FULL TEXT]
  • Treangen T, Abraham AL, Touchon M, Rocha EPC (2009) Genesis, effects and fates of repeats in prokaryotic genomes. FEMS Microbiol Rev, 33:539-71. [FULL TEXT]
  • Touchon M et al (2009) Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. PLoS Genet. 5:e1000344.[FULL TEXT ]
  • Treangen T, Ambur OH, Tonjum T, Rocha EPC (2008) The impact of the neisserial DNA uptake sequences on genome evolution and stability. Genome Biology 9:R60.[FULL TEXT]
  • Rocha EP (2008) The organization of the bacterial genome. Annu Rev Genet 42:211-33. [FULL TEXT]