title: The Oxytricha trifallax mitochondrial genome.
abstract: The Oxytricha trifallax mitochondrial genome contains the largest sequenced ciliate mitochondrial chromosome (~70 kb) plus a ~5-kb linear plasmid bearing mitochondrial telomeres. We identify two new ciliate split genes (rps3 and nad2) as well as four new mitochondrial genes (ribosomal small subunit protein genes: rps- 2, 7, 8, 10), previously undetected in ciliates due to their extreme divergence. The increased size of the Oxytricha mitochondrial genome relative to other ciliates is primarily a consequence of terminal expansions, rather than the retention of ancestral mitochondrial genes. Successive segmental duplications, visible in one of the two Oxytricha mitochondrial subterminal regions, appear to have contributed to the genome expansion. Consistent with pseudogene formation and decay, the subtermini possess shorter, more loosely packed open reading frames than the remainder of the genome. The mitochondrial plasmid shares a 251-bp region with 82% identity to the mitochondrial chromosome, suggesting that it most likely integrated into the chromosome at least once. This region on the chromosome is also close to the end of the most terminal member of a series of duplications, hinting at a possible association between the plasmid and the duplications. The presence of mitochondrial telomeres on the mitochondrial plasmid suggests that such plasmids may be a vehicle for lateral transfer of telomeric sequences between mitochondrial genomes. We conjecture that the extreme divergence observed in ciliate mitochondrial genomes may be due, in part, to repeated invasions by relatively error-prone DNA polymerase-bearing mobile elements.
authors.affiliation: Department of Ecology and Evolutionary Biology, Princeton University, USA.
authors.forename: Estienne C
authors.initials: EC
authors.lastname: Swart
authors.forename: Mariusz
authors.initials: M
authors.lastname: Nowacki
authors.forename: Justine
authors.initials: J
authors.lastname: Shum
authors.forename: Heather
authors.initials: H
authors.lastname: Stiles
authors.forename: Brian P
authors.initials: BP
authors.lastname: Higgins
authors.forename: Thomas G
authors.initials: TG
authors.lastname: Doak
authors.forename: Klaas
authors.initials: K
authors.lastname: Schotanus
authors.forename: Vincent J
authors.initials: VJ
authors.lastname: Magrini
authors.forename: Patrick
authors.initials: P
authors.lastname: Minx
authors.forename: Elaine R
authors.initials: ER
authors.lastname: Mardis
authors.forename: Laura F
authors.initials: LF
authors.lastname: Landweber
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D002874:Chromosome Mapping; D002875:Chromosomes / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D012321:DNA-Directed RNA Polymerases / Q000235:genetics; D017125:Genes, Protozoan / Q000235:genetics; D005815:Genetic Code / Q000235:genetics; D054629:Genome, Mitochondrial / Q000235:genetics*; D018503:Genome, Protozoan / Q000235:genetics*; D048648:Macronucleus / Q000201:enzymology / Q000235:genetics; D008969:Molecular Sequence Data; D016366:Open Reading Frames / Q000235:genetics; D016813:Oxytricha / Q000235:genetics*; D010957:Plasmids / Q000235:genetics; D021382:Protein Sorting Signals / Q000235:genetics; D015800:Protozoan Proteins / Q000737:chemistry / Q000235:genetics; D012335:RNA, Ribosomal / Q000235:genetics; D012343:RNA, Transfer / Q000235:genetics; D056916:Segmental Duplications, Genomic / Q000235:genetics; D026801:Synteny / Q000235:genetics
chemical_list: D004272:DNA, Mitochondrial; D021382:Protein Sorting Signals; D015800:Protozoan Proteins; D012335:RNA, Ribosomal; D012343:RNA, Transfer; D012321:DNA-Directed RNA Polymerases