Genome update: the 1000th genome – a cautionary tale

Microbiology 156 (2010), 603-608; DOI  10.1099/mic.0.038257


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.