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.

Mitochondrial Genome ofPalpitomonas bilix: Derived Genome Structure and Ancestral System for CytochromecMaturation

“…Linear mt genomes have been reported from phylogenetically diverse eukaryotes (Dinouël et al 1993; Vahrenholz et al 1993; Takano et al 1994; Fan and Lee 2002; de Graaf et al 2009; Swart et al 2012; Hikosaka et al 2013). Prior to this study on the P. bilix mt genome, there were only two known linear mt genomes bearing large inverted repeats containing multiple genes—the stramenopile Proteromonas ( Pr. )…”

Transcription-Independent Functions of an RNA Polymerase II Subunit, Rpb2, During Genome Rearrangement in the Ciliate, Oxytricha trifallax

“…After quality trimming (using Phred quality threshold 20), 12,303,838 input reads and 19,913,676 Pol-II ChIP reads were mapped to the MAC genome [17,107 full-length telomere-masked MAC chromosomes (Swart et al 2013)] and the mitochondrial genome (Swart et al 2012) with BLAT (Kent 2002), using default parameters, and then filtered for paired reads aligned in full length with at least 94% identity. ChIP and deep sequencing (ChIP-seq) reads were normalized to input by comparing number of reads mapping to the Oxytricha mitochondrial genome.…”

Putative DNA-dependent RNA polymerase in Mitochondrial Plasmid of Paramecium caudatum Stock GT704

“…Furthermore, the linear mtplasmid was found in Oxytricha trifallax (protozoa: ciliates) by Swart et al (2012). This plasmid has a size of approximately 5 kb and has 251 bp sequence with identity 82% with its mitochondrial genome (mtDNA), so it is suggested that this mtplasmid had been integrated in the mtDNA.…”