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Examples of bacterial comparative genomics
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Genome analysis of multiple pathogenic isolates of Streptococcus
agalactiae: Implications for the microbial "pan-genome". Herve
Tettelin, Vega Masignani, Michael J. Cieslewicz, Claudio Donati,
Duccio Medini, Naomi L. Ward, Samuel V. Angiuoli, Jonathan Crabtree,
Amanda L. Jones, A. Scott Durkin, Robert T. DeBoy, Tanja M. Davidsen,
Marirosa Mora, Maria Scarselli, Immaculada Margarit y Ros, Jeremy
D. Peterson, Christopher R. Hauser, Jaideep P. Sundaram, William
C. Nelson, Ramana Madupu, Lauren M. Brinkac, Robert J. Dodson, Mary
J. Rosovitz, Steven A. Sullivan, Sean C. Daugherty, Daniel H. Haft,
Jeremy Selengut, Michelle L. Gwinn, Liwei Zhou, Nikhat Zafar, Hoda
Khouri, Diana Radune, George Dimitrov, Kisha Watkins, Kevin
J. B. O'Connor, Shannon Smith, Teresa R. Utterback, Owen White, Craig
E. Rubens, Guido Grandi, Lawrence C. Madoff, Dennis L. Kasper, John
L. Telford, Michael R. Wessels, Rino Rappuoli, and Claire M. Fraser.
Proceedings of the National Academy of Science USA 2005;
102:13950-13955.
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Evolution of the core and pan-genome of Streptococcus: positive
selection, recombination, and genome composition.
Lefebure T, Stanhope MJ.
Genome Biology 2007, 8(5):R71.
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Genome-wide detection and analysis of homologous recombination
among sequenced strains of Escherichia coli.
Mau B, Glasner JD, Darling AE, Perna NT.
Genome Biology 2006;7(5):R44.
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Comparative genomics of lactic acid bacteria reveals a niche-specific
gene set.
Orla O'Sullivan, John O'Callaghan, Amaia Sangrador-Vegas, Olivia
McAuliffe, Lydia Slattery, Pawel Kaleta, Michael Callanan, Gerald F.
Fitzgerald, R. Paul Ross, and Tom Beresford.
BMC Microbiology 2009, 9:50.
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Comparative genomic analysis of plant-associated bacteria.
Van Sluys MA, Monteiro-Vitorello CB, Camargo LE, Menck CF, Da Silva
AC, Ferro JA, Oliveira MC, Setubal JC, Kitajima JP, Simpson AJ.
Annu Rev Phytopathol. 2002;40:169-89.
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Genome sequences
of three Agrobacterium biovars help elucidate the evolution of
multichromosome genomes in bacteria. Steven C. Slater, Barry
S. Goldman, Brad Goodner, Joao C. Setubal, Stephen K. Farrand, Eugene
W. Nester, Thomas J. Burr, Lois Banta, Allan W. Dickerman, Ian
Paulsen, Leon Otten, Garret Suen, Roy Welch, Nalvo F. Almeida, Frank
Arnold, Oliver T. Burton, Zijin Du, Adam Ewing, Eric Godsy, Sara
Heisel, Kathryn L. Houmiel, Jinal Jhaveri, Jing Lu, Nancy M. Miller,
Stacie Norton, Qiang Chen, Waranyoo Phoolcharoen, Victoria Ohlin, Dan
Ondrusek, Nicole Pride, Shawn L. Stricklin, Jian Sun, Cathy Wheeler,
Lindsey Wilson, Huijun Zhu, and Derek W. Wood. J. Bacteriol. April
2009 191: 2501-2511
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Trends in
Prokaryotic Evolution Revealed by Comparison of Closely Related
Bacterial and Archaeal Genomes. Pavel S. Novichkov, Yuri I. Wolf,
Inna Dubchak, and Eugene V. Koonin. J. Bacteriol. 2009 191: 65-73.
Tools and databases for bacterial comparative genomics
Mauve-related papers
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Mauve: multiple alignment of conserved genomic
sequence with rearrangements.
Aaron C.E. Darling, Bob Mau, Frederick R. Blatter, and Nicole
T. Perna.
Genome Research. 2004; 14(7):1394-1403.
Lots of information on Mauve.
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Identifying evolutionarily conserved segments among multiple divergent
and rearranged genomes. Bob Mau, Aaron E. Darling, Nicole
T. Perna. Lecture Notes in Bioinformatics 3388:72-84, Springer-Verlag
2005.
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Analyzing patterns of microbial evolution using the Mauve genome
alignment system. Aaron E. Darling, Todd J. Treangen, Xavier
Messegeur, Nicole T. Perna. Comparative Genomics (Bergman Eds.),
Springer Press, 2007.
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A fast algorithm aligning multiple microbial genomic sequences.
Guangyue Hu and Shiyi Shen.
Proceedings of the 2005 IEEE
Engineering in Medicine and Biology 27th Annual Conference.
Shanghai, China, September 1-4, 2005.
Other papers and tools
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ATGC: a database of orthologous genes from closely related
prokaryotic genomes and a research platform for microevolution of
prokaryotes.
Novichkov PS, Ratnere I, Wolf YI, Koonin EV, Dubchak I.
Nucleic Acids Res. 2009; 37(Database issue): D448-54.
The ATGC database.
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Multiple genome alignment for identifying the core structure among
moderately related microbial genomes.
Ikuo Uchiyama.
BMC Genomics. 2008; 9: 515.
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Microbial Genome Database for comparative analysis:
MBGD is a database for comparative analysis of completely sequenced
microbial genomes, the number of which is now growing rapidly. The aim
of MBGD is to facilitate comparative genomics from various points of
view such as ortholog identification, paralog clustering, motif
analysis and gene order comparison.
References: Nucleic Acids Res. 31:58-62 (2003) / Nucleic Acids
Res. 35:D343-D346 (2007)
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The UCSC archaeal genome browser
Kevin L. Schneider, Katherine S. Pollard, Robert Baertsch, Andy Pohl
and Todd M. Lowe.
Nucleic Acids Research, 2006, Vol. 34, Database issue D407-D410.
The browser.
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ACT, DNA Sequence Comparison Viewer.
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MobilomeFINDER,
A web-based tool for identifying genomic islands and other mobile DNA.
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