Skip to main content

Plant Mitochondrial Genome Diversity: The Genomics Revolution

  • Chapter
  • First Online:

Abstract

Mitochondrial genomes are remarkably diverse among green plants, and the explosion of genome sequencing over the last 30 years has greatly expanded our understanding of this diversity. Genome sizes range from 20 kilobases in some green algae to several megabases in certain angiosperms. The repertoire of genes, introns, repeats, and RNA editing is also variable, as is the amount of DNA integrated from foreign sources, including the plastid, nucleus, and other species. Genome structure is labile due to recombination involving large and small repeats, which produces multiple genomic arrangements within species and loss of synteny among species. In this review, we describe the range of diversity among plant mitochondrial genomes, discuss how the genomics revolution has advanced our understanding of this diversity, and stress the importance of future studies to resolve remaining uncertainties

This is a preview of subscription content, log in via an institution.

Buying options

Chapter
USD   29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD   129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD   169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD   169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Learn about institutional subscriptions

References

  • Adams KL, Qiu YL, Stoutemyer M, Palmer JD (2002a) Punctuated evolution of mitochondrial gene content: high and variable rates of mitochondrial gene loss and transfer to the nucleus during angiosperm evolution. Proc Natl Acad Sci USA 99:9905–9912

    PubMed  CAS  Google Scholar 

  • Adams KL, Daley DO, Whelan J, Palmer JD (2002b) Genes for two mitochondrial ribosomal proteins in flowering plants are derived from their chloroplast or cytosolic counterparts. Plant Cell 14:931–943

    PubMed  CAS  Google Scholar 

  • Allen JO, Fauron CM, Minx P, Roark L, Oddiraju S, Lin GN, Meyer L, Sun H, Kim K, Wang C, Du F, Xu D, Gibson M, Cifrese J, Clifton SW, Newton KJ (2007) Comparisons among two fertile and three male-sterile mitochondrial genomes of maize. Genetics 177:1173–1192

    PubMed  CAS  Google Scholar 

  • Alverson AJ, Wei X, Rice DW, Stern DB, Barry K, Palmer JD (2010) Insights into the evolution of mitochondrial genome size from complete sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae). Mol Biol Evol 27:1436–1448

    PubMed  CAS  Google Scholar 

  • Alverson AJ, Zhuo S, Rice DW, Sloan DB, Palmer JD (2011) The mitochondrial genome of the legume Vigna radiata and the analysis of recombination across short mitochondrial repeats. PLoS One 6:e16404

    PubMed  CAS  Google Scholar 

  • André C, Levy A, Walbot V (1992) Small repeated sequences and the structure of plant mitochondrial genomes. Trends Genet 8:128–132

    PubMed  Google Scholar 

  • Arrieta-Montiel MP, Shedge V, Davila J, Christensen AC, Mackenzie SA (2009) Diversity of the Arabidopsis mitochondrial genome occurs via nuclear-controlled recombination activity. Genetics 183:1261–1268

    PubMed  CAS  Google Scholar 

  • Bendich AJ (1985) Plant mitochondrial DNA: Unusual variation on a common theme. In: Hohn B, Dennis ES (eds) Genetic flux in plants. Springer, Wien/New York, pp 111–138

    Google Scholar 

  • Bergthorsson U, Adams KL, Thomason B, Palmer JD (2003) Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424:197–201

    PubMed  CAS  Google Scholar 

  • Bergthorsson U, Richardson AO, Young GJ, Goertzen LR, Palmer JD (2004) Massive horizontal transfer of mitochondrial genes from diverse land plant donors to the basal angiosperm Amborella. Proc Natl Acad Sci USA 101:17747–17752

    PubMed  CAS  Google Scholar 

  • Boer PH, Bonen L, Lee RW, Gray MW (1985) Genes for respiratory chain proteins and ribosomal RNAs are present on a 16-kilobase-pair DNA species from Chlamydomonas reinhardtii mitochondria. Proc Natl Acad Sci USA 82:3340–3344

    PubMed  CAS  Google Scholar 

  • Bogsch EG, Sargent F, Stanley NR, Berks BC, Robinson C, Palmer T (1998) An essential component of a novel bacterial protein export system with homologues in plastids and mitochondria. J Biol Chem 273:18003–18006

    PubMed  CAS  Google Scholar 

  • Bonen L, Gray MW (1980) Organization and expression of the mitochondrial genome of plants I. The genes for wheat mitochondrial ribosomal and transfer RNA: evidence for an unusual arrangement. Nucleic Acids Res 8:319–335

    PubMed  CAS  Google Scholar 

  • Boxma B, de Graaf RM, van der Staay GW, van Alen TA, Ricard G, Gabaldon T, van Hoek AH, Moon-van der Staay SY, Koopman WJ, van Hellemond JJ, Tielens AG, Friedrich T, Veenhuis M, Huynen MA, Hackstein JH (2005) An anaerobic mitochondrion that produces hydrogen. Nature 434:74–79

    PubMed  CAS  Google Scholar 

  • Braun H-P, Kruft V, Schmitz UK (1994) Molecular identification of the ten subunits of cytochrome-c reductase from potato mitochondria. Planta 193:99–106

    PubMed  CAS  Google Scholar 

  • Burger G, Saint-Louis D, Gray MW, Lang BF (1999) Complete sequence of the mitochondrial DNA of the red alga Porphyra purpurea. Cyanobacterial introns and shared ancestry of red and green algae. Plant Cell 11:1675–1694

    PubMed  CAS  Google Scholar 

  • Castandet B, Choury D, Begu D, Jordana X, Araya A (2010) Intron RNA editing is essential for splicing in plant mitochondria. Nucleic Acids Res 38:7112–7121

    PubMed  CAS  Google Scholar 

  • Chapdelaine Y, Bonen L (1991) The wheat mitochondrial gene for subunit I of the NADH dehydrogenase complex: a trans-splicing model for this gene-in-pieces. Cell 65:465–472

    PubMed  CAS  Google Scholar 

  • Chaw SM, Shih AC, Wang D, Wu YW, Liu SM, Chou TY (2008) The mitochondrial genome of the gymnosperm Cycas taitungensis contains a novel family of short interspersed elements, Bpu sequences, and abundant RNA editing sites. Mol Biol Evol 25:603–615

    PubMed  CAS  Google Scholar 

  • Clifton SW, Minx P, Fauron CM, Gibson M, Allen JO, Sun H, Thompson M, Barbazuk WB, Kanuganti S, Tayloe C, Meyer L, Wilson RK, Newton KJ (2004) Sequence and comparative analysis of the maize NB mitochondrial genome. Plant Physiol 136:3486–3503

    PubMed  CAS  Google Scholar 

  • Covello PS, Gray MW (1992) Silent mitochondrial and active nuclear genes for subunit 2 of cytochrome c oxidase (cox2) in soybean: evidence for RNA-mediated gene transfer. EMBO J 11:3815–3820

    PubMed  CAS  Google Scholar 

  • Cusimano N, Zhang L-B, Renner SS (2008) Reevaluation of the cox1 group I intron in Araceae and angiosperms indicates a history dominated by loss rather than horizontal transfer. Mol Biol Evol 25:265–276

    PubMed  CAS  Google Scholar 

  • Darracq A, Varre JS, Touzet P (2010) A scenario of mitochondrial genome evolution in maize based on rearrangement events. BMC Genomics 11:233

    PubMed  Google Scholar 

  • Dewey RE, Levings CS 3rd, Timothy DH (1986) Novel recombinations in the maize mitochondrial genome produce a unique transcriptional unit in the Texas male-sterile cytoplasm. Cell 44:439–449

    PubMed  CAS  Google Scholar 

  • Dombrovska O, Qiu Y-L (2004) Distribution of introns in the mitochondrial gene nad1 in land plants: phylogenetic and molecular evolutionary implications. Mol Phylogenet Evol 32:246–263

    PubMed  CAS  Google Scholar 

  • Duff RJ (2006) Divergent RNA editing frequencies in hornwort mitochondrial nad5 sequences. Gene 366:285–291

    PubMed  Google Scholar 

  • Fox TD, Leaver CJ (1981) The Zea mays mitochondrial gene coding cytochrome oxidase subunit II has an intervening sequence and does not contain TGA codons. Cell 26:315–323

    PubMed  CAS  Google Scholar 

  • Fujii S, Kazama T, Yamada M, Toriyama K (2010) Discovery of global genomic re-organization based on comparison of two newly sequenced rice mitochondrial genomes with cytoplasmic male sterility-related genes. BMC Genomics 11:209

    PubMed  Google Scholar 

  • Giegé P, Brennicke A (1999) RNA editing in Arabidopsis mitochondria effects 441 C to U changes in ORFs. Proc Natl Acad Sci USA 96:15324–15329

    PubMed  Google Scholar 

  • Giegé P, Grienenberger JM, Bonnard G (2008) Cytochrome c biogenesis in mitochondria. Mitochondrion 8:61–73

    PubMed  Google Scholar 

  • Goremykin VV, Salamini F, Velasco R, Viola R (2009) Mitochondrial DNA of Vitis vinifera and the issue of rampant horizontal gene transfer. Mol Biol Evol 26:99–110

    PubMed  CAS  Google Scholar 

  • Gray MW (2009) RNA editing in plant mitochondria: 20 years later. IUBMB Life 61:1101–1104

    PubMed  CAS  Google Scholar 

  • Gray MW, Lang BF, Burger G (2004) Mitochondria of protists. Annu Rev Genet 38:477–524

    PubMed  CAS  Google Scholar 

  • Grewe F, Viehoever P, Weisshaar B, Knoop V (2009) A trans-splicing group I intron and tRNA-hyperediting in the mitochondrial genome of the lycophyte Isoetes engelmannii. Nucleic Acids Res 37:5093–5104

    PubMed  CAS  Google Scholar 

  • Grewe F, Herres S, Viehöver P, Polsakiewicz M, Weisshaar B, Knoop V (2011) A unique transcriptome: 1782 positions of RNA editing alter 1406 codon identities in mitochondrial mRNAs of the lycophyte Isoetes engelmannii. Nucleic Acids Res 39:2890–2902

    PubMed  CAS  Google Scholar 

  • Handa H (2003) The complete nucleotide sequence and RNA editing content of the mitochondrial genome of rapeseed (Brassica napus L.): comparative analysis of the mitochondrial genomes of rapeseed and Arabidopsis thaliana. Nucleic Acids Res 31:5907–5916

    PubMed  CAS  Google Scholar 

  • Hanson MR, Bentolila S (2004) Interactions of mitochondrial and nuclear genes that affect male gametophyte development. Plant Cell 16(Suppl):S154–S169

    PubMed  CAS  Google Scholar 

  • Hao W, Palmer JD (2009) Fine-scale mergers of chloroplast and mitochondrial genes create functional, transcompartmentally chimeric mitochondrial genes. Proc Natl Acad Sci USA 106:16728–16733

    PubMed  CAS  Google Scholar 

  • Hao W, Richardson AO, Zheng Y, Palmer JD (2010) Gorgeous mosaic of mitochondrial genes created by horizontal transfer and gene conversion. Proc Natl Acad Sci USA 107:21576–21581

    PubMed  CAS  Google Scholar 

  • Heazlewood JL, Whelan J, Millar AH (2003) The products of the mitochondrial orf25 and orfB genes are FO components in the plant F1FO ATP synthase. FEBS Lett 540:201–205

    PubMed  CAS  Google Scholar 

  • Hecht J, Grewe F, Knoop V (2011) Extreme RNA editing in coding islands and abundant microsatellites in repeat sequences of Selaginella moellendorffii mitochondria: the root of frequent plant mtDNA recombination in early tracheophytes. Genome Biol Evol 3:344–358

    Google Scholar 

  • Klodmann J, Sunderhaus S, Nimtz M, Jansch L, Braun HP (2010) Internal architecture of mitochondrial complex I from Arabidopsis thaliana. Plant Cell 22:797–810

    PubMed  CAS  Google Scholar 

  • Knoop V, Schuster W, Wissinger B, Brennicke A (1991) Trans splicing integrates an exon of 22 nucleotides into the nad5 mRNA in higher plant mitochondria. EMBO J 10:3483–3493

    PubMed  CAS  Google Scholar 

  • Knoop V, Unseld M, Marienfeld J, Brandt P, Sunkel S, Ullrich H, Brennicke A (1996) copia-, gypsy- and LINE-like retrotransposon fragments in the mitochondrial genome of Arabidopsis thaliana. Genetics 142:579–585

    PubMed  CAS  Google Scholar 

  • Kobayashi Y, Knoop V, Fukuzawa H, Brennicke A, Ohyama K (1997) Interorganellar gene transfer in bryophytes: the functional nad7 gene is nuclear encoded in Marchantia polymorpha. Mol Gen Genet 256:589–592

    PubMed  CAS  Google Scholar 

  • Kubo N, Arimura S (2010) Discovery of the rpl10 gene in diverse plant mitochondrial genomes and its probable replacement by the nuclear gene for chloroplast RPL10 in two lineages of angiosperms. DNA Res 17:1–9

    PubMed  CAS  Google Scholar 

  • Kubo T, Nishizawa S, Sugawara A, Itchoda N, Estiati A, Mikami T (2000) The complete nucleotide sequence of the mitochondrial genome of sugar beet (Beta vulgaris L.) reveals a novel gene for tRNACys(GCA). Nucleic Acids Res 28:2571–2576

    PubMed  CAS  Google Scholar 

  • Lang BF, Gray MW, Burger G (1999) Mitochondrial genome evolution and the origin of eukaryotes. Annu Rev Genet 33:351–397

    PubMed  CAS  Google Scholar 

  • Leaver CJ, Gray MW (1982) Mitochondrial genome organization and expression in higher plants. Annu Rev Plant Physiol 33:373–402

    CAS  Google Scholar 

  • Leblanc C, Boyen C, Richard O, Bonnard G, Grienenberger JM, Kloareg B (1995) Complete sequence of the mitochondrial DNA of the rhodophyte Chondrus crispus (Gigartinales). Gene content and genome organization. J Mol Biol 250:484–495

    PubMed  CAS  Google Scholar 

  • Li L, Wang B, Liu Y, Qiu YL (2009) The complete mitochondrial genome sequence of the hornwort Megaceros aenigmaticus shows a mixed mode of conservative yet dynamic evolution in early land plant mitochondrial genomes. J Mol Evol 68:665–678

    PubMed  CAS  Google Scholar 

  • Lilly JW, Havey MJ (2001) Small, repetitive DNAs contribute significantly to the expanded mitochondrial genome of cucumber. Genetics 159:317–328

    PubMed  CAS  Google Scholar 

  • Lonsdale DM, Hodge TP, Fauron CM (1984) The physical map and organisation of the mitochondrial genome from the fertile cytoplasm of maize. Nucleic Acids Res 12:9249–9261

    PubMed  CAS  Google Scholar 

  • Malek O, Lättig K, Hiesel R, Brennicke A, Knoop V (1996) RNA editing in bryophytes and a molecular phylogeny of land plants. EMBO J 15:1403–1411

    PubMed  CAS  Google Scholar 

  • Maréchal A, Brisson N (2010) Recombination and the maintenance of plant organelle genome stability. New Phytol 186:299–317

    PubMed  Google Scholar 

  • Maréchal-Drouard L, Weil J-H, Guillemaut P (1988) Import of several tRNAs from the cytoplasm into the mitochondria in bean Phaseolus vulgaris. Nucleic Acids Res 16:4777–4788

    PubMed  Google Scholar 

  • Maréchal-Drouard L, Guillemaut P, Cosset A, Arbogast M, Weber F, Weil J-H, Dietrich A (1990) Transfer RNAs of potato (Solanum tuberosum) mitochondria have different genetic origins. Nucleic Acids Res 18:3689–3696

    PubMed  Google Scholar 

  • McDermott P, Connolly V, Kavanagh TA (2008) The mitochondrial genome of a cytoplasmic male sterile line of perennial ryegrass (Lolium perenne L.) contains an integrated linear plasmid-like element. Theor Appl Genet 117:459–470

    PubMed  CAS  Google Scholar 

  • Millar AH, Eubel H, Jansch L, Kruft V, Heazlewood JL, Braun HP (2004) Mitochondrial cytochrome c oxidase and succinate dehydrogenase complexes contain plant specific subunits. Plant Mol Biol 56:77–90

    PubMed  CAS  Google Scholar 

  • Mower JP (2009) The PREP suite: predictive RNA editors for plant mitochondrial genes, chloroplast genes and user-defined alignments. Nucleic Acids Res 37(Web Server issue):W253–W259

    PubMed  CAS  Google Scholar 

  • Mower JP, Bonen L (2009) Ribosomal protein L10 is encoded in the mitochondrial genome of many land plants and green algae. BMC Evol Biol 9:265

    PubMed  Google Scholar 

  • Mower JP, Palmer JD (2006) Patterns of partial RNA editing in mitochondrial genes of Beta vulgaris. Mol Genet Genomics 276:285–293

    PubMed  CAS  Google Scholar 

  • Mower JP, Touzet P, Gummow JS, Delph LF, Palmer JD (2007) Extensive variation in synonymous substitution rates in mitochondrial genes of seed plants. BMC Evol Biol 7:135

    PubMed  Google Scholar 

  • Mower JP, Stefanović S, Hao W, Gummow JS, Jain K, Ahmed D, Palmer JD (2010) Horizontal acquisition of multiple mitochondrial genes from a parasitic plant followed by gene conversion with host mitochondrial genes. BMC Biol 8:150

    PubMed  CAS  Google Scholar 

  • Notsu Y, Masood S, Nishikawa T, Kubo N, Akiduki G, Nakazono M, Hirai A, Kadowaki K (2002) The complete sequence of the rice (Oryza sativa L.) mitochondrial genome: frequent DNA sequence acquisition and loss during the evolution of flowering plants. Mol Genet Genomics 268:434–445

    PubMed  CAS  Google Scholar 

  • Nugent JM, Palmer JD (1991) RNA-mediated transfer of the gene coxII from the mitochondrion to the nucleus during flowering plant evolution. Cell 66:473–481

    PubMed  CAS  Google Scholar 

  • Nunes-Nesi A, Fernie AR (2007) Mitochondrial metabolism. In: Logan DC (ed) Plant mitochondria. Blackwell, Oxford, UK, pp 212–277

    Google Scholar 

  • Oda K, Yamato K, Ohta E, Nakamura Y, Takemura M, Nozato N, Akashi K, Kanegae T, Ogura Y, Kohchi T et al (1992) Gene organization deduced from the complete sequence of liverwort Marchantia polymorpha mitochondrial DNA. A primitive form of plant mitochondrial genome. J Mol Biol 223:1–7

    PubMed  CAS  Google Scholar 

  • Odahara M, Inouye T, Fujita T, Hasebe M, Sekine Y (2007) Involvement of mitochondrial-targeted RecA in the repair of mitochondrial DNA in the moss, Physcomitrella patens. Genes Genet Syst 82:43–51

    PubMed  CAS  Google Scholar 

  • Odahara M, Kuroiwa H, Kuroiwa T, Sekine Y (2009) Suppression of repeat-mediated gross mitochondrial genome rearrangements by RecA in the moss Physcomitrella patens. Plant Cell 21:1182–1194

    PubMed  CAS  Google Scholar 

  • Ogihara Y, Yamazaki Y, Murai K, Kanno A, Terachi T, Shiina T, Miyashita N, Nasuda S, Nakamura C, Mori N, Takumi S, Murata M, Futo S, Tsunewaki K (2005) Structural dynamics of cereal mitochondrial genomes as revealed by complete nucleotide sequencing of the wheat mitochondrial genome. Nucleic Acids Res 33:6235–6250

    PubMed  CAS  Google Scholar 

  • Ohta N, Sato N, Kuroiwa T (1998) Structure and organization of the mitochondrial genome of the unicellular red alga Cyanidioschyzon merolae deduced from the complete nucleotide sequence. Nucleic Acids Res 26:5190–5198

    PubMed  CAS  Google Scholar 

  • Oldenburg DJ, Bendich AJ (1996) Size and structure of replicating mitochondrial DNA in cultured tobacco cells. Plant Cell 8:447–461

    PubMed  CAS  Google Scholar 

  • Palmer JD, Herbon LA (1988) Plant mitochondrial DNA evolves rapidly in structure, but slowly in sequence. J Mol Evol 28:87–97

    PubMed  CAS  Google Scholar 

  • Palmer JD, Shields CR (1984) Tripartite structure of the Brassica campestris mitochondrial genome. Nature 307:437–440

    CAS  Google Scholar 

  • Picardi E, Horner DS, Chiara M, Schiavon R, Valle G, Pesole G (2010) Large-scale detection and analysis of RNA editing in grape mtDNA by RNA deep-sequencing. Nucleic Acids Res 38:4755–4767

    PubMed  CAS  Google Scholar 

  • Pombert JF, Otis C, Lemieux C, Turmel M (2004) The complete mitochondrial DNA sequence of the green alga Pseudendoclonium akinetum (Ulvophyceae) highlights distinctive evolutionary trends in the chlorophyta and suggests a sister-group relationship between the Ulvophyceae and Chlorophyceae. Mol Biol Evol 21:922–935

    PubMed  CAS  Google Scholar 

  • Pombert JF, Beauchamp P, Otis C, Lemieux C, Turmel M (2006) The complete mitochondrial DNA sequence of the green alga Oltmannsiellopsis viridis: evolutionary trends of the mitochondrial genome in the Ulvophyceae. Curr Genet 50:137–147

    PubMed  CAS  Google Scholar 

  • Richardson AO, Palmer JD (2007) Horizontal gene transfer in plants. J Exp Bot 58:1–9

    PubMed  CAS  Google Scholar 

  • Robbens S, Derelle E, Ferraz C, Wuyts J, Moreau H, Van de Peer Y (2007) The complete chloroplast and mitochondrial DNA sequence of Ostreococcus tauri: organelle genomes of the smallest eukaryote are examples of compaction. Mol Biol Evol 24:956–968

    PubMed  CAS  Google Scholar 

  • Rüdinger M, Funk HT, Rensing SA, Maier UG, Knoop V (2009) RNA editing: only eleven sites are present in the Physcomitrella patens mitochondrial transcriptome and a universal nomenclature proposal. Mol Genet Genomics 281:473–481

    PubMed  Google Scholar 

  • Ryan R, Grant D, Chiang KS, Swift H (1978) Isolation and characterization of mitochondrial DNA from Chlamydomonas reinhardtii. Proc Natl Acad Sci USA 75:3268–3272

    PubMed  CAS  Google Scholar 

  • Salmans ML, Chaw SM, Lin CP, Shih AC, Wu YW, Mulligan RM (2010) Editing site analysis in a gymnosperm mitochondrial genome reveals similarities with angiosperm mitochondrial genomes. Curr Genet 56:439–446

    PubMed  CAS  Google Scholar 

  • Sanchez-Puerta MV, Cho Y, Mower JP, Alverson AJ, Palmer JD (2008) Frequent, phylogenetically local horizontal transfer of the cox1 group I Intron in flowering plant mitochondria. Mol Biol Evol 25:1762–1777

    PubMed  CAS  Google Scholar 

  • Satoh M, Kubo T, Nishizawa S, Estiati A, Itchoda N, Mikami T (2004) The cytoplasmic male-sterile type and normal type mitochondrial genomes of sugar beet share the same complement of genes of known function but differ in the content of expressed ORFs. Mol Genet Genomics 272:247–256

    PubMed  CAS  Google Scholar 

  • Satoh M, Kubo T, Mikami T (2006) The Owen mitochondrial genome in sugar beet (Beta vulgaris L.): possible mechanisms of extensive rearrangements and the origin of the mitotype-unique regions. Theor Appl Genet 113:477–484

    PubMed  CAS  Google Scholar 

  • Schmitz-Linneweber C, Small I (2008) Pentatricopeptide repeat proteins: a socket set for organelle gene expression. Trends Plant Sci 13:663–670

    PubMed  CAS  Google Scholar 

  • Schuster W, Brennicke A (1987) Plastid, nuclear and reverse transcriptase sequences in the mitochondrial genome of Oenothera: is genetic information transferred between organelles via RNA? EMBO J 6:2857–2863

    PubMed  CAS  Google Scholar 

  • Shedge V, Arrieta-Montiel M, Christensen AC, Mackenzie SA (2007) Plant mitochondrial recombination surveillance requires unusual RecA and MutS homologs. Plant Cell 19:1251–1264

    PubMed  CAS  Google Scholar 

  • Sloan DB, Oxelman B, Rautenberg A, Taylor DR (2009) Phylogenetic analysis of mitochondrial substitution rate variation in the angiosperm tribe Sileneae. BMC Evol Biol 9:260

    PubMed  Google Scholar 

  • Sloan DB, Alverson AJ, Storchova H, Palmer JD, Taylor DR (2010a) Extensive loss of translational genes in the structurally dynamic mitochondrial genome of the angiosperm Silene latifolia. BMC Evol Biol 10:274

    PubMed  Google Scholar 

  • Sloan DB, MacQueen AH, Alverson AJ, Palmer JD, Taylor DR (2010b) Extensive loss of RNA editing sites in rapidly evolving Silene mitochondrial genomes: selection vs. retroprocessing as the driving force. Genetics 185:1369–1380

    PubMed  CAS  Google Scholar 

  • Smith DR, Lee RW (2009) The mitochondrial and plastid genomes of Volvox carteri: bloated molecules rich in repetitive DNA. BMC Genomics 10:132

    PubMed  Google Scholar 

  • Smith DR, Hua J, Lee RW (2010a) Evolution of linear mitochondrial DNA in three known lineages of Polytomella. Curr Genet 56:427–438

    PubMed  CAS  Google Scholar 

  • Smith DR, Lee RW, Cushman JC, Magnuson JK, Tran D, Polle JE (2010b) The Dunaliella salina organelle genomes: large sequences, inflated with intronic and intergenic DNA. BMC Plant Biol 10:83

    PubMed  Google Scholar 

  • Stechmann A, Hamblin K, Perez-Brocal V, Gaston D, Richmond GS, van der Giezen M, Clark CG, Roger AJ (2008) Organelles in Blastocystis that blur the distinction between mitochondria and hydrogenosomes. Curr Biol 18:580–585

    PubMed  CAS  Google Scholar 

  • Steinhauser S, Beckert S, Capesius I, Malek O, Knoop V (1999) Plant mitochondrial RNA editing. J Mol Evol 48:303–312

    PubMed  CAS  Google Scholar 

  • Stern DB, Lonsdale DM (1982) Mitochondrial and chloroplast genomes of maize have a 12-kilobase DNA sequence in common. Nature 299:698–702

    PubMed  CAS  Google Scholar 

  • Sugiyama Y, Watase Y, Nagase M, Makita N, Yagura S, Hirai A, Sugiura M (2005) The complete nucleotide sequence and multipartite organization of the tobacco mitochondrial genome: comparative analysis of mitochondrial genomes in higher plants. Mol Genet Genomics 272:603–615

    PubMed  CAS  Google Scholar 

  • Terasawa K, Odahara M, Kabeya Y, Kikugawa T, Sekine Y, Fujiwara M, Sato N (2007) The mitochondrial genome of the moss Physcomitrella patens sheds new light on mitochondrial evolution in land plants. Mol Biol Evol 24:699–709

    PubMed  CAS  Google Scholar 

  • Tian X, Zheng J, Hu S, Yu J (2006) The rice mitochondrial genomes and their variations. Plant Physiol 140:401–410

    PubMed  CAS  Google Scholar 

  • Tovar J, Fischer A, Clark CG (1999) The mitosome, a novel organelle related to mitochondria in the amitochondrial parasite Entamoeba histolytica. Mol Microbiol 32:1013–1021

    PubMed  CAS  Google Scholar 

  • Turmel M, Lemieux C, Burger G, Lang BF, Otis C, Plante I, Gray MW (1999) The complete mitochondrial DNA sequences of Nephroselmis olivacea and Pedinomonas minor. Two radically different evolutionary patterns within green algae. Plant Cell 11:1717–1730

    PubMed  CAS  Google Scholar 

  • Turmel M, Otis C, Lemieux C (2002a) The chloroplast and mitochondrial genome sequences of the charophyte Chaetosphaeridium globosum: insights into the timing of the events that restructured organelle DNAs within the green algal lineage that led to land plants. Proc Natl Acad Sci USA 99:11275–11280

    PubMed  CAS  Google Scholar 

  • Turmel M, Otis C, Lemieux C (2002b) The complete mitochondrial DNA sequence of Mesostigma viride identifies this green alga as the earliest green plant divergence and predicts a highly compact mitochondrial genome in the ancestor of all green plants. Mol Biol Evol 19:24–38

    PubMed  CAS  Google Scholar 

  • Turmel M, Otis C, Lemieux C (2003) The mitochondrial genome of Chara vulgaris: insights into the mitochondrial DNA architecture of the last common ancestor of green algae and land plants. Plant Cell 15:1888–1903

    PubMed  CAS  Google Scholar 

  • Turmel M, Otis C, Lemieux C (2007) An unexpectedly large and loosely packed mitochondrial genome in the charophycean green alga Chlorokybus atmophyticus. BMC Genomics 8:137

    PubMed  Google Scholar 

  • Turmel M, Otis C, Lemieux C (2010) A deviant genetic code in the reduced mitochondrial genome of the picoplanktonic green alga Pycnococcus provasolii. J Mol Evol 70:203–214

    Google Scholar 

  • Unseld M, Marienfeld JR, Brandt P, Brennicke A (1997) The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides. Nat Genet 15:57–61

    PubMed  CAS  Google Scholar 

  • Vangerow S, Teerkorn T, Knoop V (1999) Phylogenetic information in the mitochondrial nad5 gene of pteridophytes: RNA editing and intron sequences. Plant Biol 1:235–243

    CAS  Google Scholar 

  • Vaughn JC, Mason MT, Sper-Whitis GL, Kuhlman P, Palmer JD (1995) Fungal origin by horizontal transfer of a plant mitochondrial group I intron in the chimeric CoxI gene of Peperomia. J Mol Evol 41:563–572

    PubMed  CAS  Google Scholar 

  • Wang B, Xue J, Li L, Liu Y, Qiu YL (2009) The complete mitochondrial genome sequence of the liverwort Pleurozia purpurea reveals extremely conservative mitochondrial genome evolution in liverworts. Curr Genet 55:601–609

    PubMed  CAS  Google Scholar 

  • Ward BL, Anderson RS, Bendich AJ (1981) The mitochondrial genome is large and variable in a family of plants (Cucurbitaceae). Cell 25:793–803

    PubMed  CAS  Google Scholar 

  • Wissinger B, Schuster W, Brennicke A (1991) Trans splicing in Oenothera mitochondria: nad1 mRNAs are edited in exon and trans-splicing group II intron sequences. Cell 65:473–482

    PubMed  CAS  Google Scholar 

  • Wolfe KH, Li WH, Sharp PM (1987) Rates of nucleotide substitution vary greatly among plant mitochondrial, chloroplast, and nuclear DNAs. Proc Natl Acad Sci USA 84:9054–9058

    PubMed  CAS  Google Scholar 

  • Xue JY, Liu Y, Li L, Wang B, Qiu YL (2010) The complete mitochondrial genome sequence of the hornwort Phaeoceros laevis: retention of many ancient pseudogenes and conservative evolution of mitochondrial genomes in hornworts. Curr Genet 56:53–61

    PubMed  CAS  Google Scholar 

  • Yamamoto MP, Kubo T, Mikami T (2005) The 5′-leader sequence of sugar beet mitochondrial atp6 encodes a novel polypeptide that is characteristic of Owen cytoplasmic male sterility. Mol Genet Genomics 273:342–349

    PubMed  CAS  Google Scholar 

  • Yu W, Schuster W (1995) Evidence for a site-specific cytidine deamination reaction involved in C to U RNA editing of plant mitochondria. J Biol Chem 270:18227–18233

    PubMed  CAS  Google Scholar 

  • Zaegel V, Guermann B, Le Ret M, Andres C, Meyer D, Erhardt M, Canaday J, Gualberto JM, Imbault P (2006) The plant-specific ssDNA binding protein OSB1 is involved in the stoichiometric transmission of mitochondrial DNA in Arabidopsis. Plant Cell 18:3548–3563

    PubMed  CAS  Google Scholar 

Download references

Acknowledgements

We thank Alan Christensen, Volker Knoop, Sally Mackenzie, David Smith, Jonathan Wendel and Paul Wolf for providing comments and corrections to improve the manuscript and Wenhu Guo for help in compiling the intron distribution information in Fig. 9.5. Research in the Mower Lab on plant mitochondria is funded by the National Science Foundation (IOS-1027529 and MCB-1125386) and the University of Nebraska-Lincoln. AJA was funded by a National Institutes of Health Ruth L. Kirschstein NRSA Postdoctoral Fellowship (1F32GM080079-01A1).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Jeffrey P. Mower .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Verlag Wien

About this chapter

Cite this chapter

Mower, J.P., Sloan, D.B., Alverson, A.J. (2012). Plant Mitochondrial Genome Diversity: The Genomics Revolution. In: Wendel, J., Greilhuber, J., Dolezel, J., Leitch, I. (eds) Plant Genome Diversity Volume 1. Springer, Vienna. https://doi.org/10.1007/978-3-7091-1130-7_9

Download citation

Publish with us

Policies and ethics