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Nucleotide sequence of the mitochondrial genome of Paramecium.

ABSTRACT: The nucleotide sequence for 40,469 bp of the linear Paramecium aurelia mitochondrial (mt) genome is presented with the locations of the known genes, presumed ORFs, and their transcripts. Many of the genes commonly encoded in mt DNA of other organisms have been identified in the Paramecium mt genome but several unusual genes have been found. Ribosomal protein genes rps14, rps12, and rpl2 are clustered in a region that also contains two other genes usually found in chloroplasts, but rpl14 is over 16 kbp away. The ATP synthase gene, atp9, is encoded in this mt genome, but the atp6, atp8, and COIII genes have not been identified. All of the identified genes are transcribed. Many mono- and poly- cistronic transcripts have been detected which cover most of the genome, including large regions where genes have yet to be identified. Based on sequence comparisons with known tRNAs, only those for phe, trp, and tyr are encoded in Paramecium mt DNA.

SUBMITTER: Pritchard AE

PROVIDER: S-EPMC330218 | biostudies-other | 1990 Jan

REPOSITORIES: biostudies-other

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Nucleotide sequence of the mitochondrial genome of Paramecium.

Pritchard A E AE Seilhamer J J JJ Mahalingam R R Sable C L CL Venuti S E SE Cummings D J DJ

Nucleic acids research 19900101 1

The nucleotide sequence for 40,469 bp of the linear Paramecium aurelia mitochondrial (mt) genome is presented with the locations of the known genes, presumed ORFs, and their transcripts. Many of the genes commonly encoded in mt DNA of other organisms have been identified in the Paramecium mt genome but several unusual genes have been found. Ribosomal protein genes rps14, rps12, and rpl2 are clustered in a region that also contains two other genes usually found in chloroplasts, but rpl14 is over ...[more]

PMID: 2308823

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Project description:BACKGROUND: Despite the fact that the organization of the ciliate mitochondrial genome is exceptional, only few ciliate mitochondrial genomes have been sequenced until today. All ciliate mitochondrial genomes are linear. They are 40 kb to 47 kb long and contain some 50 tightly packed genes without introns. Earlier studies documented that the mitochondrial guanine + cytosine contents are very different between Paramecium tetraurelia and all studied Tetrahymena species. This raises the question of whether the high mitochondrial G+C content observed in P. tetraurelia is a characteristic property of Paramecium mtDNA, or whether it is an exception of the ciliate mitochondrial genomes known so far. To test this question, we determined the mitochondrial genome sequence of Paramecium caudatum and compared the gene content and sequence properties to the closely related P. tetraurelia. RESULTS: The guanine + cytosine content of the P. caudatum mitochondrial genome was significantly lower than that of P. tetraurelia (22.4% vs. 41.2%). This difference in the mitochondrial nucleotide composition was accompanied by significantly different codon usage patterns in both species, i.e. within P. caudatum clearly A/T ending codons dominated, whereas for P. tetraurelia the synonymous codons were more balanced with a higher number of G/C ending codons. Further analyses indicated that the nucleotide composition of most members of the genus Paramecium resembles that of P. caudatum and that the shift observed in P. tetraurelia is restricted to the P. aurelia species complex. CONCLUSIONS: Surprisingly, the codon usage bias in the P. caudatum mitochondrial genome, exemplified by the effective number of codons, is more similar to the distantly related T. pyriformis and other single-celled eukaryotes such as Chlamydomonas, than to the closely related P. tetraurelia. These differences in base composition and codon usage bias were, however, not reflected in the amino acid composition. Most probably, the observed picture is best explained by a hitherto unknown (neutral or adaptive) mechanism that increased the guanine + cytosine content in P. tetraurelia mtDNA on the one hand, and strong purifying selection on the ancestral amino acid composition on the other hand. These contradicting forces are counterbalanced by a considerably altered codon usage pattern.

Project description:The complete 16,043 bp mitochondrial genome (mitogenome) of Bactrocera minax (Diptera: Tephritidae) has been sequenced. The genome encodes 37 genes usually found in insect mitogenomes. The mitogenome information for B. minax was compared to the homologous sequences of Bactrocera oleae, Bactrocera tryoni, Bactrocera philippinensis, Bactrocera carambolae, Bactrocera papayae, Bactrocera dorsalis, Bactrocera correcta, Bactrocera cucurbitae and Ceratitis capitata. The analysis indicated the structure and organization are typical of, and similar to, the nine closely related species mentioned above, although it contains the lowest genome-wide A+T content (67.3%). Four short intergenic spacers with a high degree of conservation among the nine tephritid species mentioned above and B. minax were observed, which also have clear counterparts in the control regions (CRs). Correlation analysis among these ten tephritid species revealed close positive correlation between the A+T content of zero-fold degenerate sites (P0FD), the ratio of nucleotide substitution frequency at P0FD sites to all degenerate sites (zero-fold degenerate sites, two-fold degenerate sites and four-fold degenerate sites) and amino acid sequence distance (ASD) were found. Further, significant positive correlation was observed between the A+T content of four-fold degenerate sites (P4FD) and the ratio of nucleotide substitution frequency at P4FD sites to all degenerate sites; however, we found significant negative correlation between ASD and the A+T content of P4FD, and the ratio of nucleotide substitution frequency at P4FD sites to all degenerate sites. A higher nucleotide substitution frequency at non-synonymous sites compared to synonymous sites was observed in nad4, the first time that has been observed in an insect mitogenome. A poly(T) stretch at the 5' end of the CR followed by a [TA(A)]n-like stretch was also found. In addition, a highly conserved G+A-rich sequence block was observed in front of the poly(T) stretch among the ten tephritid species and two tandem repeats were present in the CR.

Dataset Information

Nucleotide sequence of the mitochondrial genome of Paramecium.

Publications

Nucleotide sequence of the mitochondrial genome of Paramecium.

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