Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark
Correspondence
David W. Ussery
(dave{at}cbs.dtu.dk)
Genomes of the month
There are four new microbial genomes listed in this month's Genome Update, three belonging to Gram-positive bacteria and one belonging to an archaeon that lives at pH 0; all of these genomes are listed in Table 1. The method of genome comparison this month is that of genome alignment and, as an example, an alignment of seven Staphylococcus aureus genomes and one Staphylococcus epidermidis genome is presented.
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The original ancestor Ames strain (Ames 0581) of Bacillus anthracis has been sequenced by The Institute for Genomic Research (TIGR) and deposited with GenBank (accession no. AE017334); a publication describing this genome is anticipated soon. The B. anthracis strain Porton (from Porton Down, UK) was used for the previously published Ames' strain genome sequence (Read et al., 2003). However, this strain had been cured of its plasmids, and subsequently the integrity of the main chromosomal sequence might have been compromised. In light of this, TIGR has sequenced Ames 0581, isolated from a dead cow in Texas in 1981, which includes the main chromosome and the plasmids pX01 and pX02. Thus, the authors are requesting that this genome be used as the reference strain in genomics studies involving comparison of B. anthracis strains.
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Method of the month alignment of bacterial genomes
There are several different ways of aligning bacterial genomes. One common method is to use MUMmer (Delcher et al., 1999). This method is fast and allows easy visualization of regions of similarity between two chromosomes; for example, an alignment between any two published microbial genomes can be viewed from TIGRs Comprehensive Microbial Resource (CMR) web pages (http://www.tigr.org). Another method is the Artemis Comparison Tool (ACT) from the Sanger Centre, which allows the comparison of multiple chromosomes. The software can be downloaded from http://www.sanger.ac.uk/Software/ACT and is fairly easy to use; for example, Fig. 1
was constructed in a single morning, using a portable Macintosh computer. This method is good for a quick visualization of regions of the chromosomes that are similar to each other.
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Supplemental web pages
Web pages containing supplemental material related to this article can be accessed from the following url: http://www.cbs.dtu.dk/services/GenomeAtlas/suppl/GenUp007/
Acknowledgements
This work was supported by a grant from the Danish National Research Foundation.
REFERENCES
Delcher, A. L., Kasif, S., Fleischmann, R. D., Peterson, J., White, O. & Salzberg, S. L. (1999). Alignment of whole genomes. Nucleic Acids Res 27, 23692376.
Feil, E. J. (2004). Small change: keeping pace with microevolution. Nat Rev Microbiol 2, 483495.[CrossRef][Medline]
Futterer, O., Angelov, A., Liesegang, H., Gottschalk, G., Schleper, C., Schepers, B., Dock, C., Antranikian, G. & Liebl, W. (2004). Genome sequence of Picrophilus torridus and its implications for life around pH 0. Proc Natl Acad Sci U S A 101, 90919096.
Holden, M. T. G., Feil, E. J., Lindsay, J. A. & 42 other authors (2004). Complete genomes of two clinical Staphylococcus aureus strains: evidence for the rapid evolution of virulence and drug resistance. Proc Natl Acad Sci U S A Epub ahead of print, doi:10.1073/pnas.0402521101
Read, T. D., Peterson, S. N., Tourasse, N. & 49 other authors (2003). The genome sequence of Bacillus anthracis Ames and comparison to closely related bacteria. Nature 423, 8186.[CrossRef][Medline]
Ussery, D. W., Hallin, P. F., Lagesen, K. & Wassenaar, T. M. (2004). Genome Update: tRNAs in sequenced microbial genomes. Microbiology 150, 16031606.[CrossRef][Medline]
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