How do we compare hundreds of bacterial genomes?

The genomic revolution is fully upon us in 2006 and the pace of discovery is set to accelerate with the emergence of ultra-high-throughput sequencing technologies. Our complete genome collection of bacteria and archaea continues to grow in number and diversity, as genome sequencing is applied to an array of new problems, from the characterization of the pan-genome to the detection of mutation after experimentation and the exploration of microbial communities in unprecedented detail. The benefits of large-scale comparative genomic analyses are driving the community to think about how to manage our public collections of genomes in novel ways.

[1]  Dawn Field,et al.  Meeting report: eGenomics: Cataloguing our Complete Genome Collection II. , 2006, Omics : a journal of integrative biology.

[2]  D. Field,et al.  Ecological perspectives on the sequenced genome collection , 2005 .

[3]  R. Edwards,et al.  A Glimpse into the Expanded Genome Content of Vibrio cholerae through Identification of Genes Present in Environmental Strains , 2005, Journal of bacteriology.

[4]  Jon R. Armstrong,et al.  Identification of genes subject to positive selection in uropathogenic strains of Escherichia coli: a comparative genomics approach. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[5]  C. Fraser,et al.  How genomics has affected the concept of microbiology. , 2005, Current opinion in microbiology.

[6]  Rolf Apweiler,et al.  Genome Reviews: standardizing content and representation of information about complete genomes. , 2006, Omics : a journal of integrative biology.

[7]  Rolf Apweiler,et al.  Evidence standards in experimental and inferential INSDC Third Party Annotation data. , 2006, Omics : a journal of integrative biology.

[8]  David W Ussery,et al.  Genome Update: annotation quality in sequenced microbial genomes. , 2004, Microbiology.

[9]  C. Médigue,et al.  MaGe: a microbial genome annotation system supported by synteny results , 2006, Nucleic acids research.

[10]  H. Tettelin,et al.  The microbial pan-genome. , 2005, Current opinion in genetics & development.

[11]  C. T. Farley,et al.  Accurate Multiplex Polony Sequencing of an Evolved Bacterial Genome , 2008 .

[12]  Dawn Field,et al.  Databases and software for the comparison of prokaryotic genomes. , 2005, Microbiology.

[13]  Naryttza N. Diaz,et al.  The Subsystems Approach to Genome Annotation and its Use in the Project to Annotate 1000 Genomes , 2005, Nucleic acids research.

[14]  B. Felden,et al.  Small RNA genes expressed from Staphylococcus aureus genomic and pathogenicity islands with specific expression among pathogenic strains. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[15]  Inna Dubchak,et al.  The integrated microbial genomes (IMG) system , 2005, Nucleic Acids Res..

[16]  Dawn Field,et al.  Cataloguing our current genome collection. , 2005, Microbiology.

[17]  J. Newman,et al.  Larger Islands House More Bacterial Taxa , 2005, Science.

[18]  K. Konstantinidis,et al.  Genomic insights that advance the species definition for prokaryotes. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[19]  D. Field,et al.  Orphans as taxonomically restricted and ecologically important genes. , 2005, Microbiology.

[20]  K. Nishikawa,et al.  Estimation of the number of authentic orphan genes in bacterial genomes. , 2004, DNA research : an international journal for rapid publication of reports on genes and genomes.

[21]  S. Clarke.  Pyrosequencing: nucleotide sequencing technology with bacterial genotyping applications , 2005, Expert review of molecular diagnostics.

[22]  Jean-Michel Claverie,et al.  FusionDB: a database for in-depth analysis of prokaryotic gene fusion events , 2004, Nucleic Acids Res..

[23]  Christa Lanz,et al.  Comprehensive mutation identification in an evolved bacterial cooperator and its cheating ancestor. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[24]  B. Snel,et al.  Toward Automatic Reconstruction of a Highly Resolved Tree of Life , 2006, Science.

[25]  D. Ussery,et al.  Genome update: distribution of two-component transduction systems in 250 bacterial genomes. , 2005, Microbiology.

[26]  G. J. Velicer,et al.  Evolution of an obligate social cheater to a superior cooperator , 2006, Nature.

[27]  Ross A. Overbeek,et al.  Automatic detection of subsystem/pathway variants in genome analysis , 2005, ISMB.

[28]  Peter F. Hallin,et al.  Ten years of bacterial genome sequencing: comparative-genomics-based discoveries , 2006, Functional & Integrative Genomics.

[29]  Owen White,et al.  Genome Properties: a system for the investigation of prokaryotic genetic content for microbiology, genome annotation and comparative genomics , 2005, Bioinform..

[30]  T. Klaenhammer,et al.  Engineered bacteriophage-defence systems in bioprocessing , 2006, Nature Reviews Microbiology.

[31]  O. White,et al.  Environmental Genome Shotgun Sequencing of the Sargasso Sea , 2004, Science.

[32]  Gordon A Anderson,et al.  Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[33]  E. Furrie,et al.  A molecular revolution in the study of intestinal microflora , 2006, Gut.

[34]  Paul B Rainey,et al.  Global analysis of predicted proteomes: functional adaptation of physical properties. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[35]  Konstantinos T. Konstantinidis,et al.  Towards a Genome-Based Taxonomy for Prokaryotes , 2005, Journal of bacteriology.

[36]  E. Rocha.  Inference and analysis of the relative stability of bacterial chromosomes. , 2006, Molecular biology and evolution.

[37]  Rodrigo Gouveia-Oliveira,et al.  Genome update: DNA repeats in bacterial genomes. , 2004, Microbiology.

[38]  Jaideep P. Sundaram,et al.  Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: implications for the microbial "pan-genome". , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[39]  G. Church,et al.  Sequencing genomes from single cells by polymerase cloning , 2006, Nature Biotechnology.

[40]  Bradford C. Powell,et al.  Similarity-based gene detection: using COGs to find evolutionarily-conserved ORFs , 2006, BMC Bioinformatics.

[41]  Nikos Kyrpides,et al.  The Genomes On Line Database (GOLD) v.2: a monitor of genome projects worldwide , 2005, Nucleic Acids Res..

[42]  Jianping Xu,et al.  INVITED REVIEW: Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances , 2006, Molecular ecology.

[43]  Richard J. Roberts,et al.  An Experimental Approach to Genome Annotation , 2004 .

[44]  David Ussery,et al.  CBS Genome Atlas Database: a dynamic storage for bioinformatic results and sequence data , 2004, Bioinform..

[45]  Rekha Seshadri,et al.  Bacterial Genomics and Pathogen Evolution , 2006, Cell.

[46]  Forest Rohwer,et al.  An application of statistics to comparative metagenomics , 2006, BMC Bioinformatics.

[47]  Masahira Hattori,et al.  Massive genome erosion and functional adaptations provide insights into the symbiotic lifestyle of Sodalis glossinidius in the tsetse host. , 2005, Genome research.

[48]  M. Breitbart,et al.  Using pyrosequencing to shed light on deep mine microbial ecology , 2006, BMC Genomics.

[49]  M. Pop,et al.  Metagenomic Analysis of the Human Distal Gut Microbiome , 2006, Science.

[50]  I. Thompson,et al.  Island size and bacterial diversity in an archipelago of engineering machines. , 2005, Environmental microbiology.