Research article
Gain and loss of an intron in a protein-coding gene in Archaea: the case of an archaeal RNA pseudouridine synthase gene
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* Corresponding author: Yoh-ichi Watanabe ywatanab@m.u-tokyo.ac.jp
1 Department of Molecular Biology, School of Life Science, Tokyo University of Pharmacy and Life Science, Horinouchi, Hachioji, Tokyo 192-0392, Japan
2 Japan Collection of Microorganisms, RIKEN (The Institute of Physical and Chemical Research) BioResource Center, Wako, Saitama 351-0198, Japan
3 Department of Biomedical Chemistry, Graduate School of Medicine, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan
4 Division of Applied Biosciences, Graduate School of Agriculture, Kyoto University, Kyoto, Kyoto 606-8502, Japan
5 Institute of Environmental Microbiology, Kyowa Kako, Tadao, Machida, Tokyo 194-0035, Japan
BMC Evolutionary Biology 2009, 9:198 doi:10.1186/1471-2148-9-198
Published: 11 August 2009Additional files
Additional file 1:
Strains and size of cbf5 intron. Details of the strains studied, including strain numbers, accession numbers, are shown.
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Additional file 2:
Oligodeoxynucleotides not listed in Table 2. Information of additional PCR and sequencing primers are shown.
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Additional file 3:
Alignment of archaeal Cbf5 sequences used in the analysis for Additional file 4. #; selected positions for the analysis.
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Additional file 4:
Bayesian phylogenetic tree of crenarchaeal Cbf5 protein. Crenarchaeal Cbf5 sequences, which are not included in Figure 2, are included.
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Additional file 5:
The results of statistical tests of analysis 1. Comparisons of statistical supports of each grouping concerning the phylogeny of the outgroups of Sulfolobales and Desulfurococcales.
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Additional file 6:
Alignment of archaeal Cbf5 sequences used in the analysis for Figure 2. #; selected positions for the analysis.
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Additional file 7:
The results of statistical tests of analysis 2. Comparisons of statistical supports of each grouping concerning the phylogeny within Sulfolobales and Desulfurococcales.
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Additional file 8:
Bayesian phylogenetic tree of the crenarchaeal 16S rRNA. This is for comparison with cbf5 tree.
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Additional file 9:
Alignment of COG1353 proteins. Sulfolobus solfataricus SSO1991, a representative of COG1353 which was predicted as a putative reverse transcriptase, and the homologs from Hyperthermus butylicus, and Ignicoccus hospitalis are included.
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Additional file 10:
Figure legends for Additional files. Legends for Additional files 3, 4, 6, 8 and 9 are shown.
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