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Hikosaka K, Watanabe YI, Tsuji N, Kita K, Kishine H, Arisue N, Palacpac NMQ, Kawazu SI, Sawai H, Horii T, Igarashi I, Tanabe K. Divergence of the mitochondrial genome structure in the apicomplexan parasites, Babesia and Theileria. Mol Biol Evol 2009; 27:1107-16. [PMID: 20034997 DOI: 10.1093/molbev/msp320] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Mitochondrial (mt) genomes from diverse phylogenetic groups vary considerably in size, structure, and organization. The genus Plasmodium, causative agent of malaria, of the phylum Apicomplexa, has the smallest mt genome in the form of a circular and/or tandemly repeated linear element of 6 kb, encoding only three protein genes (cox1, cox3, and cob). The closely related genera Babesia and Theileria also have small mt genomes (6.6 kb) that are monomeric linear with an organization distinct from Plasmodium. To elucidate the structural divergence and evolution of mt genomes between Babesia/Theileria and Plasmodium, we determined five new sequences from Babesia bigemina, B. caballi, B. gibsoni, Theileria orientalis, and T. equi. Together with previously reported sequences of B. bovis, T. annulata, and T. parva, all eight Babesia and Theileria mt genomes are linear molecules with terminal inverted repeats (TIRs) on both ends containing three protein-coding genes (cox1, cox3, and cob) and six large subunit (LSU) ribosomal RNA (rRNA) gene fragments. The organization and transcriptional direction of protein-coding genes and the rRNA gene fragments were completely conserved in the four Babesia species. In contrast, notable variation occurred in the four Theileria species. Although the genome structures of T. annulata and T. parva were nearly identical to those of Babesia, an inversion in the 3-kb central region was found in T. orientalis. Moreover, the T. equi mt genome is the largest (8.2 kb) and most divergent with unusually long TIR sequences, in which cox3 and two LSU rRNA gene fragments are located. The T. equi mt genome showed little synteny to the other species. These results suggest that the Theileria mt genome is highly diverse with lineage-specific evolution in two Theileria species: genome inversion in T. orientalis and gene-embedded long TIR in T. equi.
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Affiliation(s)
- Kenji Hikosaka
- Laboratory of Malariology, International Research Center of Infectious Diseases, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
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Hertel J, de Jong D, Marz M, Rose D, Tafer H, Tanzer A, Schierwater B, Stadler PF. Non-coding RNA annotation of the genome of Trichoplax adhaerens. Nucleic Acids Res 2009; 37:1602-15. [PMID: 19151082 PMCID: PMC2655684 DOI: 10.1093/nar/gkn1084] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2008] [Revised: 12/22/2008] [Accepted: 12/23/2008] [Indexed: 02/06/2023] Open
Abstract
A detailed annotation of non-protein coding RNAs is typically missing in initial releases of newly sequenced genomes. Here we report on a comprehensive ncRNA annotation of the genome of Trichoplax adhaerens, the presumably most basal metazoan whose genome has been published to-date. Since blast identified only a small fraction of the best-conserved ncRNAs--in particular rRNAs, tRNAs and some snRNAs--we developed a semi-global dynamic programming tool, GotohScan, to increase the sensitivity of the homology search. It successfully identified the full complement of major and minor spliceosomal snRNAs, the genes for RNase P and MRP RNAs, the SRP RNA, as well as several small nucleolar RNAs. We did not find any microRNA candidates homologous to known eumetazoan sequences. Interestingly, most ncRNAs, including the pol-III transcripts, appear as single-copy genes or with very small copy numbers in the Trichoplax genome.
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Affiliation(s)
- Jana Hertel
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraβe 16-18, D-04107 Leipzig, Division of Ecology and Evolution, Institut für Tierökologie und Zellbiologie, Tierärztliche Hochschule Hannover, Bünteweg 17d, D-30559 Hannover, Germany, Department of Theoretical Chemistry, University of Vienna, Währingerstraβe 17, A-1090 Wien, Austria, Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA, RNomics Group, Fraunhofer Institut für Zelltherapie und Immunologie, Deutscher Platz 5e, D-04103 Leipzig, Germany and Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Danielle de Jong
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraβe 16-18, D-04107 Leipzig, Division of Ecology and Evolution, Institut für Tierökologie und Zellbiologie, Tierärztliche Hochschule Hannover, Bünteweg 17d, D-30559 Hannover, Germany, Department of Theoretical Chemistry, University of Vienna, Währingerstraβe 17, A-1090 Wien, Austria, Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA, RNomics Group, Fraunhofer Institut für Zelltherapie und Immunologie, Deutscher Platz 5e, D-04103 Leipzig, Germany and Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Manja Marz
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraβe 16-18, D-04107 Leipzig, Division of Ecology and Evolution, Institut für Tierökologie und Zellbiologie, Tierärztliche Hochschule Hannover, Bünteweg 17d, D-30559 Hannover, Germany, Department of Theoretical Chemistry, University of Vienna, Währingerstraβe 17, A-1090 Wien, Austria, Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA, RNomics Group, Fraunhofer Institut für Zelltherapie und Immunologie, Deutscher Platz 5e, D-04103 Leipzig, Germany and Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Dominic Rose
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraβe 16-18, D-04107 Leipzig, Division of Ecology and Evolution, Institut für Tierökologie und Zellbiologie, Tierärztliche Hochschule Hannover, Bünteweg 17d, D-30559 Hannover, Germany, Department of Theoretical Chemistry, University of Vienna, Währingerstraβe 17, A-1090 Wien, Austria, Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA, RNomics Group, Fraunhofer Institut für Zelltherapie und Immunologie, Deutscher Platz 5e, D-04103 Leipzig, Germany and Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Hakim Tafer
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraβe 16-18, D-04107 Leipzig, Division of Ecology and Evolution, Institut für Tierökologie und Zellbiologie, Tierärztliche Hochschule Hannover, Bünteweg 17d, D-30559 Hannover, Germany, Department of Theoretical Chemistry, University of Vienna, Währingerstraβe 17, A-1090 Wien, Austria, Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA, RNomics Group, Fraunhofer Institut für Zelltherapie und Immunologie, Deutscher Platz 5e, D-04103 Leipzig, Germany and Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Andrea Tanzer
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraβe 16-18, D-04107 Leipzig, Division of Ecology and Evolution, Institut für Tierökologie und Zellbiologie, Tierärztliche Hochschule Hannover, Bünteweg 17d, D-30559 Hannover, Germany, Department of Theoretical Chemistry, University of Vienna, Währingerstraβe 17, A-1090 Wien, Austria, Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA, RNomics Group, Fraunhofer Institut für Zelltherapie und Immunologie, Deutscher Platz 5e, D-04103 Leipzig, Germany and Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Bernd Schierwater
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraβe 16-18, D-04107 Leipzig, Division of Ecology and Evolution, Institut für Tierökologie und Zellbiologie, Tierärztliche Hochschule Hannover, Bünteweg 17d, D-30559 Hannover, Germany, Department of Theoretical Chemistry, University of Vienna, Währingerstraβe 17, A-1090 Wien, Austria, Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA, RNomics Group, Fraunhofer Institut für Zelltherapie und Immunologie, Deutscher Platz 5e, D-04103 Leipzig, Germany and Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
| | - Peter F. Stadler
- Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraβe 16-18, D-04107 Leipzig, Division of Ecology and Evolution, Institut für Tierökologie und Zellbiologie, Tierärztliche Hochschule Hannover, Bünteweg 17d, D-30559 Hannover, Germany, Department of Theoretical Chemistry, University of Vienna, Währingerstraβe 17, A-1090 Wien, Austria, Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA, RNomics Group, Fraunhofer Institut für Zelltherapie und Immunologie, Deutscher Platz 5e, D-04103 Leipzig, Germany and Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA
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