Research / Scientific departments / Units and groups / Evolutionary Microbial Genomics

Microbial evolutionary genomics

Members

  • Eduardo P C Rocha, DR CNRS
  • Marie Touchon, CR CNRS
  • Julien Guglielmini, postdoc
  • Peter Chen, PhD student
  • Sophie Abby, postdoc
  • Louis-Marie Bobay, PhD student

Alumni

  • Sara Vieira-Silva, left for VIB, Be.
  • Leonor Quintais, left for the EBI, UK.
  • Todd Treangen, left for John Hopkins, US.
  • Anne-Laure Abraham, left for INRA, Fr
  • Teresa Nogueira, left for U Lisbon, Pt.
  • Chris Smillie, left for MIT, US.

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 three 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?

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.

Some recent publications

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 in press
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 in press.
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]

Touchon M, Barbier P, Bernardet JF, Loux V, Vacherie B, Barbe V, Rocha EPC, Duchaud E (2011) Complete genome sequence of the fish pathogen Flavobacterium branchiophilum. Appl Env Microbiol in press. [FULL TEXT]

Warnecke T, 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]

Touchon M, Charpentier S, Clermont O, Rocha EPC, Demanur E, Branger C. CRISPR Distribution within the Escherichia coli Species Is Not Suggestive of Immunity-Associated Diversifying Selection. J Bacteriology 193: 2460-2467. [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]

Rocha EPC, Feil EJ (2010) Mutational patterns cannot explain genome composition: are there any neutral sites in the genomes of bacteria? PLoS Genetics 6:e1001104. [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]

Abraham AL, Pothier J, Rocha EPC (2009) Alternative to Homo-oligomerisation: The Creation of Local Symmetry in Proteins by Internal Amplification. J Mol Biol 394:1683-91. [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]

Vieira-Silva S, Rocha EPC (2008) An assessment of the impacts of molecular oxygen on the evolution of proteomes. Mol Biol Evol 25:1931-42.[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]

Bailly-Bechet M, Vergassola M, Rocha EPC (2007) Causes for the intriguing presence of tRNAs in phages. Genome Res 17:1486-1495.[FULL TEXT]

Touchon M, Rocha EPC (2007) Causes of Insertion Sequences Abundance in Prokaryotic Genomes. Mol Biol Evol 24:969–981.[FULL TEXT]

Rocha EPC, Touchon M, Feil E (2006) Similar compositional biases are caused by very different mutational effects. Genome Res 16:1537-47.[FULL TEXT]

Hurst LD, Feil E, Rocha EPC (2006) Causes of trends of amino acid gain and loss. Nature 442:e11-2. [FULL TEXT]

Rocha EPC, Maynard Smith J, Hurst LD, Holden MTG, Cooper JE, Smith NH, Feil EJ (2006) Comparisons of dS / dN are time-dependent for closely related bacterial genomes. J Theoret Biol 239:226-235. [FULL TEXT]