Mitochondrial Genome of Palpitomonas bilix: Derived Genome Structure and Ancestral System for Cytochrome c Maturation.
We here reported the mitochondrial (mt) genome of one of the heterotrophic microeukaryotes related to cryptophytes, Palpitomonas bilix The P. bilix mt genome was found to be a linear molecule composed of "single copy region" (∼16 kb) and repeat regions (∼30 kb) arranged in an inverse manner at both ends of the genome. Linear mt genomes with large inverted repeats are known for three distantly related eukaryotes (including P. bilix), suggesting that this particular mt genome structure has emerged at least three times in the eukaryotic tree of life. The P. bilix mt genome contains 47 protein-coding genes including ccmA, ccmB, ccmC, and ccmF, which encode protein subunits involved in the system for cytochrome c maturation inherited from a bacterium (System I). We present data indicating that the phylogenetic relatives of P. bilix, namely, cryptophytes, goniomonads, and kathablepharids, utilize an alternative system for cytochrome c maturation, which has most likely emerged during the evolution of eukaryotes (System III). To explain the distribution of Systems I and III in P. bilix and its phylogenetic relatives, two scenarios are possible: (i) System I was replaced by System III on the branch leading to the common ancestor of cryptophytes, goniomonads, and kathablepharids, and (ii) the two systems co-existed in their common ancestor, and lost differentially among the four descendants.
Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan Present address: Japan Collection of Microorganisms/Microbe Division, RIKEN BioResource Center, Japan Collection of Microorganisms Microbe Division, Tsukuba, Japan.
Yuki
Y
Nishimura
Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan Present address: Department of Zoology, National Museum of Nature and Science, Tsukuba, Japan.
Goro
G
Tanifuji
Graduate School of Global Environmental Studies and Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan.
Ryoma
R
Kamikawa
Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan.
Akinori
A
Yabuki
Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan.
Tetsuo
T
Hashimoto
Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan yuji@ccs.tsukuba.ac.jp.
Yuji
Y
Inagaki
D001105:Archaea / Q000145:classification / Q000235:genetics*; D019843:Archaeal Proteins / Q000235:genetics*; D045304:Cytochromes c / Q000235:genetics*; D056915:DNA Copy Number Variations; D019143:Evolution, Molecular; D020745:Genome, Archaeal; D054629:Genome, Mitochondrial; D010802:Phylogeny
D019843:Archaeal Proteins; D045304:Cytochromes c
Cryptista; cytochrome c maturation; inverted repeats; mitochondrial genome