Limits...
The Oxytricha trifallax mitochondrial genome.

Swart EC, Nowacki M, Shum J, Stiles H, Higgins BP, Doak TG, Schotanus K, Magrini VJ, Minx P, Mardis ER, Landweber LF - Genome Biol Evol (2011)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Ecology and Evolutionary Biology, Princeton University, USA.

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.

Show MeSH

Related in: MedlinePlus

Segmental duplications in the 16-kb subterminal mitochondrial region of the Oxytricha mitochondrial genome long arm. The dotplot was generated by Dotmatcher (Emboss) (Rice et al. 2000) with a window size of 50 and threshold of 150. The axis scales are in base pairs. Along the axes, unknown ORFs are colored orange and known protein-coding genes are green. The ∼170-bp quadruplication is enclosed by red ellipsoids; the 1,450-bp duplication is enclosed by a blue ellipsoid. The footprint of the mO plasmid is indicated in teal; the close proximity of this site to the end of the first region that is quadruplicated is indicated by dashed lines.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3318907&req=5

fig6: Segmental duplications in the 16-kb subterminal mitochondrial region of the Oxytricha mitochondrial genome long arm. The dotplot was generated by Dotmatcher (Emboss) (Rice et al. 2000) with a window size of 50 and threshold of 150. The axis scales are in base pairs. Along the axes, unknown ORFs are colored orange and known protein-coding genes are green. The ∼170-bp quadruplication is enclosed by red ellipsoids; the 1,450-bp duplication is enclosed by a blue ellipsoid. The footprint of the mO plasmid is indicated in teal; the close proximity of this site to the end of the first region that is quadruplicated is indicated by dashed lines.

Mentions: Segmental duplications are evident from a dot plot of the ∼14.5 kb telomeric end (fig. 6). The largest of these duplications is closest to the telomeric end and is ∼1,450 bp long with ∼91% pairwise identity. An ∼170-bp region represents the sequence that has been duplicated most often. Pairwise identities relative to the first repeat (from the telomeric end) from this region decrease with increasing distance: 93.4%, 88.9%, and 74.7%. If we assume that these regions are evolving approximately neutrally, then the duplications closest to the telomeric end are younger than the distal ones. This suggests that the ∼14.5-kb region arose, in part, through successive expansions resulting in up to three successive terminal duplication events. Curiously, the 251-bp segment shared by the plasmid and mitochondrial genome is located near (∼120 bp from) the end of the most recent duplication of these repeats.


The Oxytricha trifallax mitochondrial genome.

Swart EC, Nowacki M, Shum J, Stiles H, Higgins BP, Doak TG, Schotanus K, Magrini VJ, Minx P, Mardis ER, Landweber LF - Genome Biol Evol (2011)

Segmental duplications in the 16-kb subterminal mitochondrial region of the Oxytricha mitochondrial genome long arm. The dotplot was generated by Dotmatcher (Emboss) (Rice et al. 2000) with a window size of 50 and threshold of 150. The axis scales are in base pairs. Along the axes, unknown ORFs are colored orange and known protein-coding genes are green. The ∼170-bp quadruplication is enclosed by red ellipsoids; the 1,450-bp duplication is enclosed by a blue ellipsoid. The footprint of the mO plasmid is indicated in teal; the close proximity of this site to the end of the first region that is quadruplicated is indicated by dashed lines.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3318907&req=5

fig6: Segmental duplications in the 16-kb subterminal mitochondrial region of the Oxytricha mitochondrial genome long arm. The dotplot was generated by Dotmatcher (Emboss) (Rice et al. 2000) with a window size of 50 and threshold of 150. The axis scales are in base pairs. Along the axes, unknown ORFs are colored orange and known protein-coding genes are green. The ∼170-bp quadruplication is enclosed by red ellipsoids; the 1,450-bp duplication is enclosed by a blue ellipsoid. The footprint of the mO plasmid is indicated in teal; the close proximity of this site to the end of the first region that is quadruplicated is indicated by dashed lines.
Mentions: Segmental duplications are evident from a dot plot of the ∼14.5 kb telomeric end (fig. 6). The largest of these duplications is closest to the telomeric end and is ∼1,450 bp long with ∼91% pairwise identity. An ∼170-bp region represents the sequence that has been duplicated most often. Pairwise identities relative to the first repeat (from the telomeric end) from this region decrease with increasing distance: 93.4%, 88.9%, and 74.7%. If we assume that these regions are evolving approximately neutrally, then the duplications closest to the telomeric end are younger than the distal ones. This suggests that the ∼14.5-kb region arose, in part, through successive expansions resulting in up to three successive terminal duplication events. Curiously, the 251-bp segment shared by the plasmid and mitochondrial genome is located near (∼120 bp from) the end of the most recent duplication of these repeats.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Department of Ecology and Evolutionary Biology, Princeton University, USA.

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.

Show MeSH
Related in: MedlinePlus