Macronuclear Genome Sequence of the Ciliate Tetrahymena thermophila, a Model Eukaryote |
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| Affiliation: | 1 The Institute for Genomic Research, Rockville, Maryland, United States of America, 2 Department of Biology, York University, Toronto, Ontario, Canada, 3 Centre for Research in Mass Spectrometry, York University, Toronto, Ontario, Canada, 4 Department of Biological Sciences, Marquette University, Milwaukee, Wisconsin, United States of America, 5 Razavi-Newman Center for Bioinformatics, The Salk Institute for Biological Studies, San Diego, California, United States of America, 6 Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, Illinois, United States of America, 7 Department of Biology, Harvey Mudd College, Claremont, California, United States of America, 8 Department of Biology, University of Texas at San Antonio, San Antonio, Texas, United States of America, 9 Department of Electrical Engineering, University of Texas at San Antonio, San Antonio, Texas, United States of America, 10 Department of Molecular and Cellular Biology, University of California Berkeley, Berkeley, California, United States of America, 11 Department of Computer Science and Engineering, University of Washington, Seattle, Washington, United States of America, 12 Department of Cellular Biology, University of Georgia, Athens, Georgia, United States of America, 13 Department of Biological Sciences, University of Iowa, Iowa City, Iowa, United States of America, 14 Department of Biology, University of Rochester, Rochester, New York, United States of America, 15 Canadian Institute for Advanced Research, Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada, 16 Department of Genetics, Stanford University, Stanford, California, United States of America, 17 Department of Molecular, Cellular, and Developmental Biology, University of California Santa Barbara, Santa Barbara, California, United States of America |
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| Abstract: | The ciliate Tetrahymena thermophila is a model organism for molecular and cellular biology. Like other ciliates, this species has separate germline and soma functions that are embodied by distinct nuclei within a single cell. The germline-like micronucleus (MIC) has its genome held in reserve for sexual reproduction. The soma-like macronucleus (MAC), which possesses a genome processed from that of the MIC, is the center of gene expression and does not directly contribute DNA to sexual progeny. We report here the shotgun sequencing, assembly, and analysis of the MAC genome of T. thermophila, which is approximately 104 Mb in length and composed of approximately 225 chromosomes. Overall, the gene set is robust, with more than 27,000 predicted protein-coding genes, 15,000 of which have strong matches to genes in other organisms. The functional diversity encoded by these genes is substantial and reflects the complexity of processes required for a free-living, predatory, single-celled organism. This is highlighted by the abundance of lineage-specific duplications of genes with predicted roles in sensing and responding to environmental conditions (e.g., kinases), using diverse resources (e.g., proteases and transporters), and generating structural complexity (e.g., kinesins and dyneins). In contrast to the other lineages of alveolates (apicomplexans and dinoflagellates), no compelling evidence could be found for plastid-derived genes in the genome. UGA, the only T. thermophila stop codon, is used in some genes to encode selenocysteine, thus making this organism the first known with the potential to translate all 64 codons in nuclear genes into amino acids. We present genomic evidence supporting the hypothesis that the excision of DNA from the MIC to generate the MAC specifically targets foreign DNA as a form of genome self-defense. The combination of the genome sequence, the functional diversity encoded therein, and the presence of some pathways missing from other model organisms makes T. thermophila an ideal model for functional genomic studies to address biological, biomedical, and biotechnological questions of fundamental importance. |
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