title: Comparative mitogenomics indicates respiratory competence in parasitic Viscum despite loss of complex I and extreme sequence divergence, and reveals horizontal gene transfer and remarkable variation in genome size.
abstract: Aerobically respiring eukaryotes usually contain four respiratory-chain complexes (complexes I-IV) and an ATP synthase (complex V). In several lineages of aerobic microbial eukaryotes, complex I has been lost, with an alternative, nuclear-encoded NADH dehydrogenase shown in certain cases to bypass complex I and oxidize NADH without proton translocation. The first loss of complex I in any multicellular eukaryote was recently reported in two studies; one sequenced the complete mitogenome of the hemiparasitic aerial mistletoe, Viscum scurruloideum, and the other sequenced the V. album mitogenome. The V. scurruloideum study reported no significant additional loss of mitochondrial genes or genetic function, but the V. album study postulated that mitochondrial genes encoding all ribosomal RNAs and proteins of all respiratory complexes are either absent or pseudogenes, thus raising questions as to whether the mitogenome and oxidative respiration are functional in this plant.
  
  
  
  To determine whether these opposing conclusions about the two Viscum mitogenomes reflect a greater degree of reductive/degenerative evolution in V. album or instead result from interpretative and analytical differences, we reannotated and reanalyzed the V. album mitogenome and compared it with the V. scurruloideum mitogenome. We find that the two genomes share a complete complement of mitochondrial rRNA genes and a typical complement of genes encoding respiratory complexes II-V. Most Viscum mitochondrial protein genes exhibit very high levels of divergence yet are evolving under purifying, albeit relaxed selection. We discover two cases of horizontal gene transfer in V. album and show that the two Viscum mitogenomes differ by 8.6-fold in size (66 kb in V. scurruloideum; 565 kb in V. album).
  
  
  
  Viscum mitogenomes are extraordinary compared to other plant mitogenomes in terms of their wide size range, high rates of synonymous substitutions, degree of relaxed selection, and unprecedented loss of respiratory complex I. However, contrary to the initial conclusions regarding V. album, both Viscum mitogenomes possess conventional sets of rRNA and, excepting complex I, respiratory genes. Both plants should therefore be able to carry out aerobic respiration. Moreover, with respect to size, the V. scurruloideum mitogenome has experienced a greater level of reductive evolution.
authors.affiliation: Department of Biology, Indiana University, Bloomington, IN, 47405, USA.|Present address: Department of Bioinformatics and Computational Biology, Genentech Inc., 1 DNA Way, South San Francisco, CA, 94080, USA.
authors.forename: Elizabeth
authors.initials: E
authors.lastname: Skippington
authors.affiliation: Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, 49008, USA.
authors.forename: Todd J
authors.initials: TJ
authors.lastname: Barkman
authors.affiliation: Department of Biology, Indiana University, Bloomington, IN, 47405, USA.
authors.forename: Danny W
authors.initials: DW
authors.lastname: Rice
authors.affiliation: Department of Biology, Indiana University, Bloomington, IN, 47405, USA. jpalmer@indiana.edu.
authors.forename: Jeffrey D
authors.initials: JD
authors.lastname: Palmer
mesh_terms: D018744:DNA, Plant; D045222:Electron Transport Chain Complex Proteins / Q000235:genetics; D042967:Electron Transport Complex I / Q000235:genetics* / Q000378:metabolism; D019143:Evolution, Molecular; D017353:Gene Deletion; D022761:Gene Transfer, Horizontal; D017343:Genes, Plant; D014644:Genetic Variation; D054629:Genome, Mitochondrial; D018745:Genome, Plant; D058977:Molecular Sequence Annotation; D010940:Plant Proteins / Q000235:genetics; D018749:RNA, Plant; D012335:RNA, Ribosomal; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D028181:Viscum / Q000235:genetics* / Q000378:metabolism; D028182:Viscum album / Q000235:genetics / Q000378:metabolism
chemical_list: D018744:DNA, Plant; D045222:Electron Transport Chain Complex Proteins; D010940:Plant Proteins; D018749:RNA, Plant; D012335:RNA, Ribosomal; D042967:Electron Transport Complex I
keywords: Complex I; Mistletoes; Mitogenome; Mutation rate; Parasitic plants; Respiratory competence