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Archaea, 2:137–143
© 2007 Heron Publishing—Victoria, Canada
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Gene decay in archaea

M. W. J. van Passel (1, 2), C. S. Smillie (1) and H. Ochman (1)

1. Department of Biochemistry and Molecular Biophysics, University of Arizona, 1007 East Lowell Street, Tucson, AZ 85721, USA / 2. Corresponding author ([email protected]) / Received November 17, 2006; accepted February 19, 2007; published online March 7, 2007


The gene-dense chromosomes of archaea and bacteria were long thought to be devoid of pseudogenes, but with the massive increase in available genome sequences, whole genome comparisons between closely related species have identified mutations that have rendered numerous genes inactive. Comparative analyses of sequenced archaeal genomes revealed numerous pseudogenes, which can constitute up to 8.6% of the annotated coding sequences in some genomes. The largest proportion of pseudogenes is created by gene truncations, followed by frameshift mutations. Within archaeal genomes, large numbers of pseudogenes contain more than one inactivating mutation, suggesting that pseudogenes are deleted from the genome more slowly in archaea than in bacteria. Although archaea seem to retain pseudogenes longer than do bacteria, most archaeal genomes have unique repertoires of pseudogenes.

Keywords: comparative genomics, pseudogenes.

 ISSN 1472-3654 (Online) ISSN 1472-3646 (Print) Copyright © 2002–2007 Heron Publishing