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A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans

Mircea Podar1*, Iain Anderson2, Kira S Makarova3, James G Elkins1, Natalia Ivanova2, Mark A Wall4, Athanasios Lykidis2, Kostantinos Mavromatis2, Hui Sun2, Matthew E Hudson48, Wenqiong Chen49, Cosmin Deciu4, Don Hutchison4, Jonathan R Eads4, Abraham Anderson104, Fillipe Fernandes4, Ernest Szeto2, Alla Lapidus2, Nikos C Kyrpides2, Milton H Saier5, Paul M Richardson2, Reinhard Rachel6, Harald Huber6, Jonathan A Eisen7, Eugene V Koonin3, Martin Keller1 and Karl O Stetter6

Author Affiliations

1 Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd, Oak Ridge, TN 37831, USA

2 DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA 94598, USA

3 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 8600 Rockville Pike, Bethesda, MD 20894, USA

4 Verenium Corporation, 4955 Directors Place, San Diego CA 92121, USA

5 Division of Biological Sciences, University of California San Diego, 9500 Gilman Drive, La Jolla, CA 92037, USA

6 Lehrstuhl für Mikrobiologie und Archaeenzentrum, Universität Regensburg, Universitätstraße 31, Regensburg, D-93053, Germany

7 Genome Center, University of California Davis, One Shields Avenue, Davis, CA 95616, USA

8 Current address: College of Agricultural, Consumer, and Environmental Sciences University of Illinois at Urbana-Champaign, 1101 W Peabody Dr., Urbana, IL 61801, USA

9 Current address: Biology Department, San Diego State University, 5500 Campanile Drive San Diego, CA 92182, USA

10 Current address: Amgen Inc., One Amgen Center Drive, Thousand Oaks, CA 91320, USA

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Genome Biology 2008, 9:R158  doi:10.1186/gb-2008-9-11-r158

Published: 10 November 2008

Abstract

Background

The relationship between the hyperthermophiles Ignicoccus hospitalis and Nanoarchaeum equitans is the only known example of a specific association between two species of Archaea. Little is known about the mechanisms that enable this relationship.

Results

We sequenced the complete genome of I. hospitalis and found it to be the smallest among independent, free-living organisms. A comparative genomic reconstruction suggests that the I. hospitalis lineage has lost most of the genes associated with a heterotrophic metabolism that is characteristic of most of the Crenarchaeota. A streamlined genome is also suggested by a low frequency of paralogs and fragmentation of many operons. However, this process appears to be partially balanced by lateral gene transfer from archaeal and bacterial sources.

Conclusions

A combination of genomic and cellular features suggests highly efficient adaptation to the low energy yield of sulfur-hydrogen respiration and efficient inorganic carbon and nitrogen assimilation. Evidence of lateral gene exchange between N. equitans and I. hospitalis indicates that the relationship has impacted both genomes. This association is the simplest symbiotic system known to date and a unique model for studying mechanisms of interspecific relationships at the genomic and metabolic levels.