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1 Comparative Genomics 2.7 Paper II: Ten years of bacterial genome sequencing: comparative–genomics–based discoveries
Funct Integr Genomics (2006) 6: 165–185 DOI 10.1007/s10142-006-0027-2 REVIEW Tim T. Binnewies . Yair Motro . Peter F. Hallin . Ole Lund . David Dunn . Tom La . David J. Hampson . Matthew Bellgard . Trudy M. Wassenaar . David W. Ussery Ten years of bacterial genome sequencing: comparative-genomics-based discoveries Received: 20 January 2006 / Revised: 24 February 2006 / Accepted: 7 March 2006 / Published online: 12 May 2006 # Springer-Verlag 2006 Abstract It has been more than 10 years since the first bacterial genome sequence was published. Hundreds of bacterial genome sequences are now available for comparative genomics, and searching a given protein against more than a thousand genomes will soon be possible. The subject of this review will address a relatively straightforward question: “What have we learned from this vast amount of new genomic data?” Perhaps one of the most important lessons has been that genetic diversity, at the level of large-scale variation amongst even genomes of the same species, is far greater than was thought. The classical textbook view of evolution relying on the relatively slow accumulation of mutational events at the level of individual bases scattered throughout the genome has changed. One of the most obvious conclusions from examining the sequences from several hundred bacterial genomes is the enormous amount of diversity—even in different genomes from the same bacterial species. This diversity is generated by a variety of mechanisms, including mobile genetic elements and bacteriophages. An examination of the 20 Escherichia coli genomes sequenced so far dramatically illustrates this, with the genome size ranging from 4.6 to 5.5 Mbp; much of the variation appears to be of phage origin. This review also addresses mobile genetic elements, T. T. Binnewies . P. F. Hallin . O. Lund . D. W. Ussery (*) Center for Biological Sequence Analysis, Technical University of Denmark, 2800 Lyngby, Denmark e-mail: dave@cbs.dtu.dk Y. Motro . D. Dunn . M. Bellgard Center for Bioinformatics and Biological Computing, Murdoch University, Murdoch, Western Australia 6150, Australia T. La . D. J. Hampson School of Veterinary and Biomedical Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia T. M. Wassenaar Molecular Microbiology and Genomics Consultants, Zotzenheim, Germany including pathogenicity islands and the structure of transposable elements. There are at least 20 different methods available to compare bacterial genomes. Metagenomics offers the chance to study genomic sequences found in ecosystems, including genomes of species that are difficult to culture. It has become clear that a genome sequence represents more than just a collection of gene sequences for an organism and that information concerning the environment and growth conditions for the organism are important for interpretation of the genomic data. The newly proposed Minimal Information about a Genome Sequence standard has been developed to obtain this information. Keywords Bacterial genomics . Comparative genomics . Bioinformatics . Genomic diversity . Molecular evolution Introduction The year 1995 marked the publication of two human pathogenic bacterial genome sequences: Haemophilus influenzae (Fleischmann et al. 1995, US patent number 6,528,289) and Mycoplasma genetalium (Fraser et al. 1995, US patent number 6,537,773). Since then, more than 300 bacterial genomes have been fully sequenced and become publicly available, including the sequence of a virulent form of H. influenzae (Harrison et al. 2005); the original H. influenzae strain sequenced in 1995 was from an isolate that does not cause disease. Although the majority of these several hundred genomes are from pathogenic organisms, some environmental bacterial genome sequences have also become available. This review article will provide a brief overview of sequenced bacterial genomes, their genomic diversity and some of the insights gained from analysis of this vast amount of data. Bacteria are microscopic unicellular prokaryotes that inhabit a wide variety of environmental niches, broadly distributed in three ecosystems: the soil, marine environments and other living organisms. Although there are
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Peter Fischer Hallin | 2009 Peter F
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1 Comparative Genomics 2.10 Paper V
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4314 74 Tools Abstract: Of the plet
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4316 74 Tools Size distribution of
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4318 74 Tools Genome atlas Intrinsi
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4320 74 Tools Genome atlas Intrinsi
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4322 74 Tools for Comparison of Bac
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4324 74 Tools for Comparison of Bac
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4326 74 Tools information, as genet
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Chapter 3 rRNA operons and promoter
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RNA operons and promoter analysis O
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Code Meaning Example C Coding CCCCC
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1 rRNA operons and promoter analysi
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Using HMMs also simplifies the use
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of the annotation. Some of the majo
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where match states stop around 10 c
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1 rRNA operons and promoter analysi
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synthesis in flow cells to simultan
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Read absence. A boolean where ‘on
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Hallin, et al. Figure 4 | The dataf
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Genome homology: Comparing multiple
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ing platform-‐independent Java
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34. Wang H, Noordewier M, Benham CJ
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Chapter 4 Web Services and Interope
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Web Services and Interoperability i
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Chapter 5 Conclusion and perspectiv
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Appendix A Appendix: Workshops, tea
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Appendix B Appendix: Ph.D. study pl
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Danmarks Tekniske Universitet AFI,
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Danmarks Tekniske Universitet AFI,
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Appendix C Appendix: Courses C.1 Gl
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D.2 Sample output from queryGenomes
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Appendix: Software 13 w a r n " $ o
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Appendix: Software 109 m y ( $ m i
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Appendix: Software 25 [ ] A l t e r
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BIBLIOGRAPHY J. Rogers, P. F. Stadl
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BIBLIOGRAPHY Q. Jin, Z. Yuan, J. Xu
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BIBLIOGRAPHY Velicer, F.-J. Vorholt
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