Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, Lyngby, DK-2800, Denmark
Correspondence
David W. Ussery
(dave{at}cbs.dtu.dk)
Bacterial genomes are now being published almost every week. The purpose of this new column is to provide monthly updates on new genomes which have been published, as well as to discuss methods for genome comparison of the more than 100 bacterial genomes which are already publicly available. Thus, each column will be divided into two parts, with the first part devoted to a brief description of highlights of the recently sequenced genomes and the second part devoted to a discussion of relevant methods currently being used to compare sequenced genomes to each other. Each month a table will be presented, as shown in Table 1, with the name, length, AT content, number of rRNAs, tRNAs, CDS regions annotated and accession numbers for each new genome. The genome sequences of four species have been published in the first half of December 2003: Vibrio vulnificus, a marine pathogen, the cyanobacterium Gloeobacter violaceus, the soil bacterium Geobacter sulfurreducens and the plant pathogen Phytoplasma asteris.
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The Geobacter sulfurreducens strain PCA genome contains a single circular chromosome of 3 814 139 bp (Methé et al., 2003). Geobacter sulfurreducens is a member of the
-Proteobacteria and, as such, its genome sequence is the first of this subdivision to be published. [Desulfovibrio vulgaris subsp. vulgaris str. Hildenborough is also a member of the
-Proteobacteria and its genome was sequenced by TIGR more than 2 years ago (October 2001), but the genome report has yet to be published at the time of writing this article (December 2003). However, BLAST searches against this genome are possible (GenBank accession no. NC_002937)]. Geobacter sulfurreducens can be used in bioremediation of groundwater. This is due to the ability of this species of bacteria to precipitate soluble metals, such as uranium. Based on the genome sequence, it looks as though Geobacter sulfurreducens might not be immobile, nor a strict anaerobe, as had been thought previously. The genome also contains an unprecedented collection of newly reported c-type cytochromes (Methé et al., 2003
).
Finally, P. asteris is an obligate intracellular plant pathogen, transmitted by insects, and its genome is the first of a bacterium inhabiting both plants and insects to be sequenced. The genome of the P. asteris strain OY contains a circular chromosome of 860 631 bp (Oshima et al., 2003). The genome has undergone reductive evolution and there are many genes thought to be essential for life, such as the ATP-synthase subunits, which are missing in this organism. Although almost twice as large as the smallest genome sequenced so far, the contents of the P. asteris genome are important to take into consideration when contemplating the minimal genome of life.
Method of the month
Perhaps one of the simplest ways of comparing many genomes is simply to list them in a table, with rows of various numbers describing each genome (such as length, AT content, number of genes, etc., as in Table 1). Of course, it is obvious that a genome cannot be fully reduced to a single number. But some characteristics, such as the length of the chromosome, AT content, fraction of repeats and number of genes, are at least a good place to start in comparison of a large number of genomes. As an example, of the genomes presented in Table 1
, looking at the number of rRNA operons, the Gloeobacter violaceus genome has only a single rRNA operon, compared to nine rRNA operons in the V. vulnificus genome. There is certainly a difference in lifestyle of the two organisms whilst a single Gloeobacter violaceus cell is lazily replicating under the alpine sun, over a period of about 3 days (72 h), V. vulnificus can have an in vivo doubling time of about 45 min (Starks et al., 2000
). Thus, a single V. vulnificus cell can undergo about 100 cell divisions, yielding about 6x1029 cells, during the same time it would take one Gloeobacter violaceus cell to divide into two cells. Obviously, the Vibrio cells will need to make much more rRNA for such rapid growth. Thus, the number of rRNA operons in a genome can be reflective of information about the relative doubling time of the organism.
At the time of writing this article, there are 144 sequenced bacterial genomes and 17 archaeal genomes that are available to the public. These can be viewed on our web page and sorted by various data, including the date of publication (http://www.cbs.dtu.dk/services/GenomeAtlas). About 50 of the 144 public bacterial genomes have been made available during 2003 and it is very likely that more than 100 bacterial genomes will become available in 2004. There are about twice as many bacterial genome sequences (250) that can be searched against using BLAST (http://www.ncbi.nlm.nih.gov/sutils/genom_table.cgi?) than can be downloaded from GenBank or EMBL (128 genomes; http://www.ebi.ac.uk/genomes/bacteria.html). Currently, it takes a year (or longer) between the time a genome is sequenced and the time that it is fully annotated and a detailed report is written about the project, so there is a lag between the time a genome is sequenced and when it is published. The growth in the number of prokaryotic genome sequences published in recent years is shown in Fig. 1. It is worth noting that, although archaeal species probably exist in equal abundance with bacterial species, to date comparatively few archaeal genomes have been sequenced. The publication of so many genome sequences has led to an explosion of genomic information, which can be difficult to keep up with. In fact, as can be seen from the V. vulnificus genomes of the two different strains mentioned above, sometimes even people within the field can miss projects where other groups have sequenced the same organism and deposited it in GenBank.
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ACKNOWLEDGEMENTS
This work was supported by a grant from the Danish National Research Foundation.
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