title: Gene Loss and Error-Prone RNA Editing in the Mitochondrion of Perkinsela, an Endosymbiotic Kinetoplastid.
abstract: Perkinsela is an enigmatic early-branching kinetoplastid protist that lives as an obligate endosymbiont inside Paramoeba (Amoebozoa). We have sequenced the highly reduced mitochondrial genome of Perkinsela, which possesses only six protein-coding genes (cox1, cox2, cox3, cob, atp6, and rps12), despite the fact that the organelle itself contains more DNA than is present in either the host or endosymbiont nuclear genomes. An in silico analysis of two Perkinsela strains showed that mitochondrial RNA editing and processing machineries typical of kinetoplastid flagellates are generally conserved, and all mitochondrial transcripts undergo U-insertion/deletion editing. Canonical kinetoplastid mitochondrial ribosomes are also present. We have developed software tools for accurate and exhaustive mapping of transcriptome sequencing (RNA-seq) reads with extensive U-insertions/deletions, which allows detailed investigation of RNA editing via deep sequencing. With these methods, we show that up to 50% of reads for a given edited region contain errors of the editing system or, less likely, correspond to alternatively edited transcripts.
  
  
  OBJECTIVE
  Uridine insertion/deletion-type RNA editing, which occurs in the mitochondrion of kinetoplastid protists, has been well-studied in the model parasite genera Trypanosoma, Leishmania, and Crithidia. Perkinsela provides a unique opportunity to broaden our knowledge of RNA editing machinery from an evolutionary perspective, as it represents the earliest kinetoplastid branch and is an obligatory endosymbiont with extensive reductive trends. Interestingly, up to 50% of mitochondrial transcripts in Perkinsela contain errors. Our study was complemented by use of newly developed software designed for accurate mapping of extensively edited RNA-seq reads obtained by deep sequencing.
authors.affiliation: Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic.
authors.forename: Vojtěch
authors.initials: V
authors.lastname: David
authors.affiliation: Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.
authors.forename: Pavel
authors.initials: P
authors.lastname: Flegontov
authors.affiliation: Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.
authors.forename: Evgeny
authors.initials: E
authors.lastname: Gerasimov
authors.affiliation: Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada.
authors.forename: Goro
authors.initials: G
authors.lastname: Tanifuji
authors.affiliation: Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic.
authors.forename: Hassan
authors.initials: H
authors.lastname: Hashimi
authors.affiliation: Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow, Russia.
authors.forename: Maria D
authors.initials: MD
authors.lastname: Logacheva
authors.affiliation: Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada.
authors.forename: Shinichiro
authors.initials: S
authors.lastname: Maruyama
authors.affiliation: Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada.
authors.forename: Naoko T
authors.initials: NT
authors.lastname: Onodera
authors.affiliation: Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada Canadian Institute for Advanced Research, Toronto, Canada.
authors.forename: Michael W
authors.initials: MW
authors.lastname: Gray
authors.affiliation: Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada Canadian Institute for Advanced Research, Toronto, Canada.
authors.forename: John M
authors.initials: JM
authors.lastname: Archibald
authors.affiliation: Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic Canadian Institute for Advanced Research, Toronto, Canada jula@paru.cas.cz.
authors.forename: Julius
authors.initials: J
authors.lastname: Lukeš
mesh_terms: D056894:Amoebozoa / Q000469:parasitology; D019295:Computational Biology; D004272:DNA, Mitochondrial / Q000737:chemistry / Q000235:genetics; D017353:Gene Deletion; D059014:High-Throughput Nucleotide Sequencing; D016830:Kinetoplastida / Q000235:genetics* / Q000254:growth & development; D008928:Mitochondria / Q000235:genetics*; D017393:RNA Editing; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial