title: A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes.
abstract: Analyses of 55 individual and 31 concatenated protein data sets encoded in Reclinomonas americana and Marchantia polymorpha mitochondrial genomes revealed that current methods for constructing phylogenetic trees are insufficiently sensitive (or artifact-insensitive) to ascertain the sister of mitochondria among the current sample of eight alpha-proteobacterial genomes using mitochondrially-encoded proteins. However, Rhodospirillum rubrum came as close to mitochondria as any alpha-proteobacterium investigated. This prompted a search for methods to directly compare eukaryotic genomes to their prokaryotic counterparts to investigate the origin of the mitochondrion and its host from the standpoint of nuclear genes. We examined pairwise amino acid sequence identity in comparisons of 6,214 nuclear protein-coding genes from Saccharomyces cerevisiae to 177,117 proteins encoded in sequenced genomes from 45 eubacteria and 15 archaebacteria. The results reveal that approximately 75% of yeast genes having homologues among the present prokaryotic sample share greater amino acid sequence identity to eubacterial than to archaebacterial homologues. At high stringency comparisons, only the eubacterial component of the yeast genome is detectable. Our findings indicate that at the levels of overall amino acid sequence identity and gene content, yeast shares a sister-group relationship with eubacteria, not with archaebacteria, in contrast to the current phylogenetic paradigm based on ribosomal RNA. Among eubacteria and archaebacteria, proteobacterial and methanogen genomes, respectively, shared more similarity with the yeast genome than other prokaryotic genomes surveyed.
authors.affiliation: Institute of Botany III, University of Düsseldorf, Düsseldorf, Germany.
authors.forename: Christian
authors.initials: C
authors.lastname: Esser
authors.forename: Nahal
authors.initials: N
authors.lastname: Ahmadinejad
authors.forename: Christian
authors.initials: C
authors.lastname: Wiegand
authors.forename: Carmen
authors.initials: C
authors.lastname: Rotte
authors.forename: Federico
authors.initials: F
authors.lastname: Sebastiani
authors.forename: Gabriel
authors.initials: G
authors.lastname: Gelius-Dietrich
authors.forename: Katrin
authors.initials: K
authors.lastname: Henze
authors.forename: Ernst
authors.initials: E
authors.lastname: Kretschmann
authors.forename: Erik
authors.initials: E
authors.lastname: Richly
authors.forename: Dario
authors.initials: D
authors.lastname: Leister
authors.forename: David
authors.initials: D
authors.lastname: Bryant
authors.forename: Michael A
authors.initials: MA
authors.lastname: Steel
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Lockhart
authors.forename: David
authors.initials: D
authors.lastname: Penny
authors.forename: William
authors.initials: W
authors.lastname: Martin
mesh_terms: D020561:Alphaproteobacteria / Q000235:genetics*; D001105:Archaea / Q000235:genetics; D001419:Bacteria / Q000235:genetics*; D001426:Bacterial Proteins / Q000235:genetics; D002352:Carrier Proteins / Q000235:genetics; D019143:Evolution, Molecular; D019766:Genes, Archaeal; D005798:Genes, Bacterial; D005800:Genes, Fungal; D016678:Genome; D008928:Mitochondria / Q000235:genetics; D024101:Mitochondrial Proteins / Q000235:genetics; D008957:Models, Genetic; D010802:Phylogeny; D012247:Rhodospirillum rubrum / Q000235:genetics; D012441:Saccharomyces cerevisiae / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics; D017386:Sequence Homology, Amino Acid
chemical_list: D001426:Bacterial Proteins; D002352:Carrier Proteins; D024101:Mitochondrial Proteins; D029701:Saccharomyces cerevisiae Proteins