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
Four new genomes will be discussed in this month's Genome Update. The list of organisms given in Table 1 includes an archaeon, two bacteria and an eukaryote. Two genomes will only be mentioned briefly. The protozoan Cryptosporidium hominis causes gastroenteritis and diarrhoea around the world. Like the Cryptosporidium parvum genome (Abrahamsen et al., 2004
), that of C. hominis has undergone genome reduction to a size of about 9 Mbp, and both genomes have slightly fewer than 4000 genes (Xu et al., 2004
). Photobacterium profundum is a member of the vibrio group (Thompson et al., 2004
), and its genome consists of two chromosomes and one plasmid (Table 1
). At the time of writing, the GenBank files have been deposited, but the genome report has not yet been published. One very interesting feature of this genome is the larger number of rRNAs.
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Method of the month: visualizing proteome comparisons
This month we will present two ways of comparing bacterial proteomes (i.e. all the proteins encoded by a genome); both methods are based on the identification of sequence homologies in protein sequences, detected by BLASTP.
We have collected all annotated proteins of all eight Mycoplasma genome sequences currently available, and blasted each of the individual sequences against the collection. For each organism, we extracted the number of genes distinct for that organism and the number of genes shared with the other species. These two numbers are shown in Fig. 1(a), and reflect to some extent an evolutionary distance or similarity between the individual species. The large circle in the middle represents a pool of all 6053 proteins from the Mycoplasma genomes. The smaller intersecting bubbles represent the individual Mycoplasma genomes, and the area (size) is proportional to the total number of proteins for that genome. The intersecting areas illustrate the number of homologues between a given genome and the pool of proteins, excluding hits from the genome itself. (Otherwise, all of the proteins would have a hit!) Only hits having an E-value of 1015 or better were included. One interesting observation is that there seems to be a core set of roughly 500 proteins for each genome that is found in at least one other Mycoplasma. We have measured how many species the average gene has orthologues to the connectivity. For each gene in every genome, we have counted the number of genomes that this gene has homology to and divided it by the species count (7); the resulting number ranges between 0 (0/7, found in no other species) and 1 (7/7, are found in all other species). The average for each genome is located at the bottom of each circle, and ranges from 0·58 to 0·71. On the other hand, the number of organism-specific proteins encoded by the various Mycoplasma genomes varies ranging from around 500 (513 for Mycoplasma mycoides, 500 for Mycoplasma penetrans) to a mere five (for Mycoplasma genitalium).
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In addition to these results, we have generated a neighbour-joining tree based on 16S rRNA gene sequences of all species, using CLUSTAL_X. The relatively short evolutionary distance for M. genitalium and Mycoplasma pneumoniae could be an explanation as to why these two species have not developed or acquired many distinct genes compared with other species. It is our anticipation to develop a web-based platform on our Genome Atlas web pages that will allow for BLASTP proteome comparisons such as these between any chosen set of sequenced microbial genomes. Readers are encouraged to check the supplemental web page for updates and links to this service when it is operational.
Supplemental web pages
Web pages containing material related to this article can be accessed from the following url: http://www.cbs.dtu.dk/services/GenomeAtlas/suppl/GenUp012/
Acknowledgements
This work was supported by a grant from the Danish National Research Foundation.
REFERENCES
Abrahamsen, M. S., Templeton, T. J., Enomoto, S. & 17 other authors (2004). Complete genome sequence of the apicomplexan, Cryptosporidium parvum. Science 304, 441445.
Baliga, N. S., Bonneau, R., Facciotti, M. T. & 12 other authors (2004). Genome sequence of Haloarcula marismortui: a halophilic archaeon from the Dead Sea. Genome Res 14, 22212234.
Minion, F. C., Lefkowitz, E. J., Madsen, M. L., Cleary, B. J., Swartzell, S. M. & Mahairas, G. G. (2004). The genome sequence of Mycoplasma hyopneumoniae strain 232, the agent of swine mycoplasmosis. J Bacteriol 186, 71237133.
Thompson, F. L., Iida, T. & Swings, J. (2004). Biodiversity of vibrios. Microbiol Mol Biol Rev 68, 403431.
Waites, K. B. & Talkington, D. F. (2004). Mycoplasma pneumoniae and its role as a human pathogen. Clin Microbiol Rev 17, 697728.
Xu, P., Widmer, G., Wang, Y. & 15 other authors (2004). The genome of Cryptosporidium hominis. Nature 431, 11071112.[CrossRef][Medline]
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