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Genome update: the 1000th genome--a cautionary tale
Karin Lagesen1,2, Dave W Ussery2, Trudy M Wassenaar3,2
1Centre for Molecular Biology and Neuroscience, Institute of Medical Microbiology, Oslo University Hospital, Rikshospitalet, NO-0027, Oslo, Norway, and Department of Informatics, University of Oslo, PO Box 1080 Blindern, NO-0316, Oslo, Norway.
Microbiology (Reading, England)
|January 23, 2010
Summary
Analysis of over 1000 prokaryotic genomes reveals vast biological diversity. Surprisingly, no single protein is conserved across all bacterial genomes, highlighting unique evolutionary paths.
Area of Science:
- Genomics
- Microbiology
- Bioinformatics
Background:
- Over 1000 prokaryotic genomes are publicly available for analysis.
- Public sequence databases (GenBank, DDBJ, EMBL) exhibit minor content discrepancies due to logistical issues.
- Inaccurate data on widely accessed web pages can lead to erroneous conclusions, such as misidentifying the largest bacterial genome.
Purpose of the Study:
- To assess the extent of biological diversity within sequenced prokaryotic genomes.
- To identify conserved genes across all bacterial and archaeal genomes.
- To highlight potential inaccuracies in public genomic databases.
Main Methods:
- Comparative analysis of over 1000 prokaryotic genome sequences from public databases.
- Examination of gene families and conserved proteins across diverse bacterial species.
- Identification of universally conserved genes in bacteria, excluding Archaea.
Main Results:
- Prokaryotic biological diversity is significantly greater than previously estimated.
- Analysis of multiple Escherichia coli genomes suggests approximately 45,000 gene families, exceeding the human genome.
- Not a single protein is conserved across all 1000 sequenced genomes.
- Excluding Archaea, only four genes (two protein, two RNA) are conserved in all bacteria.
Conclusions:
- The vast genomic diversity among prokaryotes necessitates careful data curation in public databases.
- The limited number of universally conserved genes underscores the unique evolutionary trajectories of bacterial lineages.
- Further research is needed to refine our understanding of core bacterial genes and genome evolution.
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