Genome update: the 1000th genome – a cautionary tale

摘要

There are now more than 1000 sequenced prokaryotic genomes deposited inpublic databases and available for analysis. Currently, although the sequencedatabases GenBank, DNA Database of Japan and EMBL are synchronized continually,there are slight differences in content at the genomes level for a varietyof logistical reasons, including differences in format and loading errors,such as those caused by file transfer protocol interruptions. This means thatthe 1000th genome will be different in the various databases. Some of thedata on the highly accessed web pages are inaccurate, leading to false conclusionsfor example about the largest bacterial genome sequenced. Biological diversityis far greater than many have thought. For example, analysis of multiple Escherichia coli genomes has led to an estimate of around 45 000 genefamilies — more genes than are recognized in the human genome. Moreover,of the 1000 genomes available, not a single protein is conserved across allgenomes. Excluding the members of the Archaea, only a total of fourgenes are conserved in all bacteria: two protein genes and two RNA genes.