Nucleic Acids Research Advance Access originally published online on October 23, 2008
Nucleic Acids Research 2008 36(21):6688-6719; doi:10.1093/nar/gkn668
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Nucleic Acids Research, 2008, Vol. 36, No. 21 6688-6719
© 2008 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
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Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
*To whom correspondence should be addressed. Tel: +1 301 435 5913; Fax: +1 301 480 9241; Email: koonin{at}ncbi.nlm.nih.gov
Received June 23, 2008. Revised September 15, 2008. Accepted September 22, 2008.
The first bacterial genome was sequenced in 1995, and the first archaeal genome in 1996. Soon after these breakthroughs, an exponential rate of genome sequencing was established, with a doubling time of approximately 20 months for bacteria and approximately 34 months for archaea. Comparative analysis of the hundreds of sequenced bacterial and dozens of archaeal genomes leads to several generalizations on the principles of genome organization and evolution. A crucial finding that enables functional characterization of the sequenced genomes and evolutionary reconstruction is that the majority of archaeal and bacterial genes have conserved orthologs in other, often, distant organisms. However, comparative genomics also shows that horizontal gene transfer (HGT) is a dominant force of prokaryotic evolution, along with the loss of genetic material resulting in genome contraction. A crucial component of the prokaryotic world is the mobilome, the enormous collection of viruses, plasmids and other selfish elements, which are in constant exchange with more stable chromosomes and serve as HGT vehicles. Thus, the prokaryotic genome space is a tightly connected, although compartmentalized, network, a novel notion that undermines the ‘Tree of Life’ model of evolution and requires a new conceptual framework and tools for the study of prokaryotic evolution.
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