Evoldeep publication:
Philippe Deschamps; Yvan Zivanovic; David Moreira; Francisco Rodriguez-Valera; Purificacion Lopez-Garcia
Pangenome evidence for extensive inter-domain horizontal transfer affecting lineage-core and shell genes in uncultured planktonic Thaumarchaeota and Euryarchaeota
Genome Biology and Evolution 2014; doi: 10.1093/gbe/evu127
Abstract: http://gbe.oxfordjournals.org/cgi/content/abstract/evu127? ijkey=j1xJIn7qlzlDtz9&keytype=ref
PDF: http://gbe.oxfordjournals.org/cgi/reprint/evu127? ijkey=j1xJIn7qlzlDtz9&keytype=refPrevious partner publications in relation with the subject (2004-2008):
Bolhuis H, Palm P, Wende A, Falb M, Rampp M, Rodriguez-Valera F, Pfeiffer F, Oesterhelt D. (2006) The genome of the square archaeon Haloquadratum walsbyi: life at the limits of water activity. BMC Genomics 7:169.
Brochier-Armanet C, Boussau B, Gribaldo S, Forterre P (2008) Mesophilic crenarchaeota: proposal for a third archaeal phylum, the Thaumarchaeota Nature Reviews Microbiology. 6:245-252
Brochier-Armanet C and Forterre F (2007) Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers Archaea. 2:83-93
Brochier C, Forterre P, Gribaldo S (2005) An emerging phylogenetic core of Archaea: phylogenies of transcription and translation machineries converge following addition of new genome sequences BMC Evol Biol. 5(1):36
Brochier C, Gribaldo S, Zivanovic Y, Confalonieri F, Forterre P (2005) Nanoarchaea: representatives of a novel archaeal phylum or a fast-evolving euryarchaeal lineage related to Thermococcales? Genome Biology. 6(5):R42
Cuadros-Orellana S, Martin-Cuadrado AB, Legault B, D'Auria G, Zhaxybayeva O, Papke RT, Rodriguez-Valera F. (2007) Genomic plasticity in prokaryotes: the case of the square haloarchaeon. ISME J1:235-45.
Gribaldo S and Brochier-Armanet C (2006) The origin and evolution of Archaea: a state of the art Philos Trans R Soc Lond B Biol Sci. 361(1470):1007-22
López-García, P., Brochier, C., Moreira, D. & Rodríguez-Valera F. (2004) Comparative analysis of a genome fragment of an uncultivated mesopelagic crenarchaeote reveals multiple horizontal gene transfers, Environ Microbiol, 6:19-34.
Martín-Cuadrado, A., Rodríguez-Valera, F., Moreira, D., Alba, JC, Ivars-Martinez, E., Henn, M.R., Talla, E., and López-García, P. (2008) Hindsight in the relative abundance, metabolic potential and genome dynamics of uncultivated marine archaea from comparative metagenomic analyses of bathypelagic plankton of different oceanic regions. ISME J, 2: 865-886.
Martín-Cuadrado, A., López-García, P., Alba, JC, Moreira, D., Monticelli, L., Strittmatter, A., Gottschalk, G., and Rodríguez-Valera, F. (2007) Metagenomics of the deep Mediterranean, a warm bathypelagic habitat. PLoS ONE 2(9): e914.
Moreira, D., Rodríguez-Valera F. & López-García, P. (2004) Analysis of a genome fragment of a deep-sea uncultivated Group II euryarchaeote containing 16S rDNA, a spectinomycin operon and several energy metabolism genes, Environ Microbiol, 6: 959-969.
Moreira, D., Rodríguez-Valera, P. & López-García, P. (2006) Genome fragments from mesopelagic Antarctic waters reveal a novel deltaproteobacterial group related to the myxobacteria. Microbiology, 152: 505-517.
Moussard, H., G. Henneke, D. Moreira, V. Jouffe, P. López-García, and C. Jeanthon (2006) A thermophilic lifestyle for an uncultured archaeon of the DHVE2 lineage: Evidence from environmental genomics. Applied Environ. Microbiol. 72: 2268-2271.
Moussard, H., D. Moreira, M.A. Cambon-Bonavita, P. López-García, and C. Jeanthon (2006) Uncultured Archaea in a hydrothermal microbial assemblage: Phylogenetic diversity and characterization of a genome fragment from a euryarchaeote. FEMS Microbiol. Ecol. 57: 452-469.
Quaiser, A., López-García, P., Zivanovic, Y., Rodriguez-Valera, F., Henn, M.R. & Moreira, D. (2008) Comparative analysis of genome fragments of Acidobacteria from deep Mediterranean plankton, Environ Microbiol. 10: 2704-2717
Sanchez-Perez, G. Mira, A. Nyiro, G. Pasic, L. and Rodriguez-Valera F. (2008) Adaptation of the Salinibacter ruber proteome to changing salinity by specialized paralogs: the concept of ecoparalogs. Trends in Genetics. 24: 154-158.
Zivanovic Y, Lopez P, Philippe H, Forterre P. (2002) Pyrococcus genome comparison evidences chromosome shuffling-driven evolution. Nucleic Acids Res. 30:1902-1910.