Ecophysiological significance of scale-dependent patterns in prokaryotic genomes unveiled by a combination of statistic and genometric analyses

6 páginas, 3 figuras.We combined genometric (DNA walks) and statistical (detrended fluctuation analysis) methods on 456 prokaryotic chromosomes from 309 different bacterial and archaeal species to look for specific patterns and long-range correlations along the genome and relate them to ecological lifestyles. The position of each nucleotide along the complete genome sequence was plotted on an orthogonal plane (DNA landscape), and fluctuation analysis applied to the DNA walk series showed a long-range correlation in contrast to the lack of correlation for artificially generated genomes. Different features in the DNA landscapes among genomes from different ecological and metabolic groups of prokaryotes appeared with the combined analysis. Transition from hyperthermophilic to psychrophilic environments could have been related to more complex structural adaptations in microbial genomes, whereas for other environmental factors such as pH and salinity this effect would have been smaller. Prokaryotes with domain-specific metabolisms, such as photoautotrophy in Bacteria and methanogenesis in Archaea, showed consistent differences in genome correlation structure. Overall, we show that, beyond the relative proportion of nucleotides, correlation properties derived from their sequential position within the genome hide relevant phylogenetic and ecological information. This can be studied by combining genometric and statistical physics methods, leading to a reduction of genome complexity to a few useful descriptors.This work was financed by Projects VIARC REN2003-08333 and CRENYC CGL2006-12058 to E.O.C. and Grant SAF2004-06134 to J.G. from the Spanish Ministerio de Educación y Ciencia, Marine Genomics Europe Network of Excellence Grant GOCE-CT-2003-505403 from the EU-FP6 (to E.O.C.), and Thematic Network on Environmental Microbial Genomics Grant 2004-XT-00012 from the Autonomous Government of Catalonia (to E.O.C.). We are very grateful to the staff at the Department of Physics, Boston University, for their help in running calculations and to the Centre de Supercomputació de Catalunya (www.cesca.es) for supercomputing facilities. Constructive comments from the reviewers are also acknowledged. J.A.G. is supported by an FI predoctoral scholarship and a travel grant to Boston from the Catalonian Departament d’Universitats, Recerca i Societat de la Informació, and by Marine Genomics Europe training courses on bioinformatics. E.O.C. is a Fellow of the Program Ramon y Cajal from the Spanish Ministerio de Educación y Ciencia and FEDER.Peer reviewe

Ecophysiological significance of scale-dependent patterns in prokaryotic genomes unveiled by a combination of statistic and genometric analyses

6 páginas, 3 figuras.We combined genometric (DNA walks) and statistical (detrended fluctuation analysis) methods on 456 prokaryotic chromosomes from 309 different bacterial and archaeal species to look for specific patterns and long-range correlations along the genome and relate them to ecological lifestyles. The position of each nucleotide along the complete genome sequence was plotted on an orthogonal plane (DNA landscape), and fluctuation analysis applied to the DNA walk series showed a long-range correlation in contrast to the lack of correlation for artificially generated genomes. Different features in the DNA landscapes among genomes from different ecological and metabolic groups of prokaryotes appeared with the combined analysis. Transition from hyperthermophilic to psychrophilic environments could have been related to more complex structural adaptations in microbial genomes, whereas for other environmental factors such as pH and salinity this effect would have been smaller. Prokaryotes with domain-specific metabolisms, such as photoautotrophy in Bacteria and methanogenesis in Archaea, showed consistent differences in genome correlation structure. Overall, we show that, beyond the relative proportion of nucleotides, correlation properties derived from their sequential position within the genome hide relevant phylogenetic and ecological information. This can be studied by combining genometric and statistical physics methods, leading to a reduction of genome complexity to a few useful descriptors.This work was financed by Projects VIARC REN2003-08333 and CRENYC CGL2006-12058 to E.O.C. and Grant SAF2004-06134 to J.G. from the Spanish Ministerio de Educación y Ciencia, Marine Genomics Europe Network of Excellence Grant GOCE-CT-2003-505403 from the EU-FP6 (to E.O.C.), and Thematic Network on Environmental Microbial Genomics Grant 2004-XT-00012 from the Autonomous Government of Catalonia (to E.O.C.). We are very grateful to the staff at the Department of Physics, Boston University, for their help in running calculations and to the Centre de Supercomputació de Catalunya (www.cesca.es) for supercomputing facilities. Constructive comments from the reviewers are also acknowledged. J.A.G. is supported by an FI predoctoral scholarship and a travel grant to Boston from the Catalonian Departament d’Universitats, Recerca i Societat de la Informació, and by Marine Genomics Europe training courses on bioinformatics. E.O.C. is a Fellow of the Program Ramon y Cajal from the Spanish Ministerio de Educación y Ciencia and FEDER.Peer reviewe