Genome update: the 1000th genome--a cautionary tale.
There are now more than 1000 sequenced prokaryotic genomes deposited in public databases and available for analysis. Currently, although the sequence databases GenBank, DNA Database of Japan and EMBL are synchronized continually, there are slight differences in content at the genomes level for a variety of logistical reasons, including differences in format and loading errors, such as those caused by file transfer protocol interruptions. This means that the 1000th genome will be different in the various databases. Some of the data on the highly accessed web pages are inaccurate, leading to false conclusions for example about the largest bacterial genome sequenced. Biological diversity is far greater than many have thought. For example, analysis of multiple Escherichia coli genomes has led to an estimate of around 45 000 gene families - more genes than are recognized in the human genome. Moreover, of the 1000 genomes available, not a single protein is conserved across all genomes. Excluding the members of the Archaea, only a total of four genes are conserved in all bacteria: two protein genes and two RNA genes.
Lagesen
Karin
K
Centre 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.|Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, 2800 Lyngby, Denmark.
Ussery
Dave W
DW
Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, 2800 Lyngby, Denmark.
Wassenaar
Trudy M
TM
Molecular Microbiology and Genomics Consultants, Zotzenheim, Germany.|Center for Biological Sequence Analysis, Department of Systems Biology, The Technical University of Denmark, 2800 Lyngby, Denmark.
D055028:Comparative Genomic Hybridization; D030561:Databases, Nucleic Acid; D005798:Genes, Bacterial; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D023281:Genomics; D017422:Sequence Analysis, DNA