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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

Additional files

Additional data file 1:

Table S1: the inferred creanarchaeal core genes lost by I. hospitalis. Table S2: functional categories gained and lost in the I. hospitalis genome. Table S3: functional gene categories (arCOGs) present in N. equitans but absent in I. hospitalis and their distribution in archaeal genomes. Table S4: the gene family expansions in the I. hospitalis genome.

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Additional data file 2:

Figure S1: a phylogenetic tree of cultivated thermophilic species of Crenarchaeota based on SSU rRNA sequences. Figure S2: phylogenetic trees of archaeal tyrosyl-tRNA synthetases and of family IV endonucleases. Figure S3: a phylogenetic tree of the alpha subunit of archaeal 2-oxoacid: ferredoxin oxidoreductases. Figure S4: amino acid-based sequence alignment of conserved regions of the alpha and beta subunits of pyruvate:ferredoxin oxidoreductases and OGORs.

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Additional data file 3:

Numerical and classification data associated with all the bacterial and archaeal genomes used in genome size analysis.

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Additional data file 4:

Protein sequence alignments used to infer lateral gene transfer of valyl t-RNA synthetase, leucyl aminopeptidase, tyrosyl t-RNA synthetase and endonuclease IV, in phylip format.

Format: PHY Size: 43KB Download file

Open Data