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Nucleic Acids Research, 2003, Vol. 31, No. 6 1673-1682
© 2003 Oxford University Press

Complete sequence of the mitochondrial genome of Tetrahymena thermophila and comparative methods for identifying highly divergent genes

Clifford F. Brunk, Louis C. Lee, Anne B. Tran and Jinliang Li1

Department of Organismic Biology, Ecology and Evolution, University of California–Los Angeles, Los Angeles, CA 90095-1606, USA and 1 Laragen Inc., 10755 Venice Boulevard, Los Angeles, CA 90034, USA

*To whom correspondence should be addressed. Tel: +1 310 825 3114; Fax: +1 310 206 3987; Email: cbrunk{at}ucla.edu

The complete sequence of the mitochondrial genome of Tetrahymena thermophila has been determined and compared with the mitochondrial genome of Tetrahymena pyriformis. The sequence similarity clearly indicates homology of the entire T.thermophila and T.pyriformis mitochondrial genomes. The T.thermophila genome is very compact, most of the intergenic regions are short (only three are longer than 63 bp) and comprise only 3.8% of the genome. The nad9 gene is tandemly duplicated in T.thermophila. Long terminal inverted repeats and the nad9 genes are undergoing concerted evolution. There are 55 putative genes: three ribosomal RNA genes, eight transfer RNA genes, 22 proteins with putatively assigned functions and 22 additional open reading frames of unknown function. In order to extend indications of homology beyond amino acid sequence similarity we have examined a number of physico-chemical properties of the mitochondrial proteins, including theoretical pI, molecular weight and particularly the predicted transmembrane spanning regions. This approach has allowed us to identify homologs to ymf58 (nad4L), ymf62 (nad6) and ymf60 (rpl6).


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