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Organellar Genomes of Flowering Plants

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Abstract

Arguably, the two most important organelles of the eukaryotic cell are not its original inhabitants. Mitochondria and chloroplasts have evolved by endo symbiosis and have a prokaryotic ancestry. This is reflected perfectly in their genome organization and the basic functioning of their genetic system. Over the long course of evolution, they have given away most of their genes. The genes were either lost because they were no longer needed or were relocated to the nucleus. Nuclear transfer of their DNA is an ongoing process, and the two organellar genomes are still evolving. The DNA sequences are in a constant state of motion because of interorganellar and horizontal gene transfer within and between different plant species. In contrast to the chloroplast genomes, which are much conserved and do not generally exhibit any structural or functional anomalies, mitochondria are notorious for their lack of synteny, frequent DNA rearrangements, constantly varying intergenic regions and accumulation of heterologous DNA sequences. Since the nucleus cannot work in isolation, all the random and mischievous genetic activities of organellar genomes have had a direct or indirect impact on nuclear genome evolution. They act as one of the major mechanisms by which genetic novelty is brought about in the nuclear genome. As they say, to produce good music, both black and white chords have to work in harmony. Similarly, irrespective of individual nature of the three genomes in a cell, these three always work in harmony for optimum functioning of the plant cell.

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References

  • Abdelnoor RV, Yule R, Elo A, Christensen AC, Gauen GM, Mackenzie SA (2003) Substoichiometric shifting in the plant mitochondrial genome is influenced by a gene homologous to MutS. Proc Natl Acad Sci U S A 100(10):5968–5973

    CAS  PubMed Central  PubMed  Google Scholar 

  • Adams KL, Palmer JD (2003) Evolution of mitochondrial gene content: gene loss and transfer to the nucleus. Mol Phylogenet Evol 29(3):380–395

    CAS  PubMed  Google Scholar 

  • Adams KL, Song K, Roessler PG, Nugent JM, Doyle JL, Doyle JJ, Palmer JD (1999) Intracellular gene transfer in action: dual transcription and multiple silencings of nuclear and mitochondrial cox2 genes in legumes. Proc Natl Acad Sci U S A 96:13863–13868

    CAS  PubMed Central  PubMed  Google Scholar 

  • Adams KL, Daley DO, Qiu YL, Whelan J, Palmer JD (2000) Repeated, recent and diverse transfers of a mitochondrial gene to the nucleus in flowering plants. Nature 408:354–357

    CAS  PubMed  Google Scholar 

  • Ahlert D, Stegemann S, Kahlau S, Ruf S, Bock R (2009) Insensitivity of chloroplast gene expression to DNA methylation. Mol Genet Genomics 282:17–24

    CAS  PubMed Central  PubMed  Google Scholar 

  • Ali MA, Gyulai G, Hidvegi N, Kerti B, Hemaid FMAA, Pandey AK, Lee J (2014) The changing epitome of species identification – DNA barcoding. Saudi J Biol Sci 21:204–231

    Google Scholar 

  • Allen JF (1993a) Control of gene expression by redox potential and the requirement for chloroplast and mitochondrial genomes. J Theor Biol 165:609–631

    CAS  PubMed  Google Scholar 

  • Allen JF (1993b) Redox control of gene expression and the function of chloroplast genomes: a hypothesis. Photosynth Res 36:95–102

    CAS  PubMed  Google Scholar 

  • Allen JF (2003) The function of genomes in bioenergetic organelles. Philos Trans R Soc Lond B (eds). Biol Sci 358:19–37

    Google Scholar 

  • Allen JO, Fauron CM, Minx P, Roark L et al (2007) Comparisons among two fertile and three male-sterile mitochondrial genomes of maize. Genetics 177:1173–1192

    CAS  PubMed Central  PubMed  Google Scholar 

  • Alverson AJ, Wei XX, 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(6):1436–1448

    CAS  PubMed Central  PubMed  Google Scholar 

  • Alverson AJ, Rice DW, Dickinson S, Barry K, Palmera JD (2011a) Origins and recombination of the bacterial-sized multichromosomal mitochondrial genome of cucumber. Plant Cell 23:2499–2513

    CAS  PubMed Central  PubMed  Google Scholar 

  • Alverson AJ, Zhuo S, Rice DW, Sloan DB, Palmer JD (2011b) The mitochondrial genome of the legume Vigna radiata and the analysis of recombination across short mitochondrial repeats. PLoS One 6(1):e16404

    CAS  PubMed Central  PubMed  Google Scholar 

  • Arimura S, Yamamoto J, Aida GP, Nakazono M, Tsutsumi N (2004) Frequent fusion and fission of plant mitochondria with unequal nucleoid distribution. Proc Natl Acad Sci U S A 101(20):7805–7808

    CAS  PubMed Central  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

    CAS  PubMed Central  PubMed  Google Scholar 

  • Backert S, Nielsen BL, Börner T (1997) The mystery of the rings: structure and replication of mitochondrial genomes from higher plants. Trends Plant Sci 2:477–483

    Google Scholar 

  • Barbrook AC, Howe CJ, Purton S (2006) Why are plastid genomes retained in non-photosynthetic organisms? Trends Plant Sci 11(2):101–108

    CAS  PubMed  Google Scholar 

  • Barbrook AC, Howe CJ, Kurniawan DP, Tarr SJ (2010) Organization and expression of organellar genomes. Philos Trans R Soc B 365:785–797

    CAS  Google Scholar 

  • Baur E (1909) Zeit. Vererbungsl 1:330–351

    Google Scholar 

  • Bendich AJ (1993) Reaching for the ring: the study of mitochondrial genome structure. Curr Genet 24(4):279–290

    CAS  PubMed  Google Scholar 

  • Bendich AJ (2004) Circular chloroplast chromosomes: the grand illusion. Plant Cell 16:1661–1666

    CAS  PubMed Central  PubMed  Google Scholar 

  • Bensasson D, Zhang DX, Hartl DL, Hewi GM (2001) Mitochondrial pseudogenes: evolution’s misplaced witnesses. Trends Ecol Evol 16(6):314–321

    PubMed  Google Scholar 

  • Bergthorsson U, Adams KL, Thomason B, Palmer JD (2003) Widespread horizontal transfer of mitochondrial genes in flowering plants. Nature 424(6945):197–201

    CAS  PubMed  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 U S A 101(51):17747–17752

    CAS  PubMed Central  PubMed  Google Scholar 

  • Birky CW Jr (2008) Uniparental inheritance of organelle genes. Curr Biol 16:R1–R4

    Google Scholar 

  • Blanchard JL, Lynch M (2000) Organellar genes why do they end up in the nucleus? Trends Genet 16(7):315–320

    CAS  PubMed  Google Scholar 

  • Bock R (2009) The give-and-take of DNA: horizontal gene transfer in plants. Trends Plant Sci 15:11–22

    PubMed  Google Scholar 

  • Bonen L (2008) Cis- and trans-splicing of group II introns in plant mitochondria. Mitochondrion 8(1):26–34

    CAS  PubMed  Google Scholar 

  • Boore JL (1999) Animal mitochondrial genomes. Nucl Acids Res 27(8):1767–1780

    CAS  PubMed Central  PubMed  Google Scholar 

  • Brennicke A, Grohmann L, Hiesel R, Knoop V, Schuster W (1993) The mitochondrial genome on its way to the nucleus: different stages of gene transfer in higher plants. FEBS Lett 325(1–2):140–145

    CAS  PubMed  Google Scholar 

  • Burton WG, Grabowy CT, Sager R (1979) Role of methylation in the modification and restriction of chloroplast DNA in Chlamydomonas. Proc Natl Acad Sci U S A 76(3):1390–1394

    CAS  PubMed Central  PubMed  Google Scholar 

  • CBOL Plant Working Group (2009) A DNA barcode for land plants. Proc Natl Acad Sci U S A 106(31):12794–12797

    PubMed Central  Google Scholar 

  • Chang S, Wang Y, Lu J, Gai J, Li J et al (2013) The mitochondrial genome of soybean reveals complex genome structures and gene evolution at intercellular and phylogenetic levels. PLoS One 8(6):1–14

    Google Scholar 

  • Chiu WL, Stubbe W, Sears BB (1988) Plastid inheritance in Oenothera: organelle genome modifies the extent of biparental transmission. Curr Genet 13:181–189

    CAS  Google Scholar 

  • Cho Y, Qiu Y, Kuhlman P, Palmer JD (1998) Explosive invasion of plant mitochondria by a group I intron. Proc Natl Acad Sci U S A 95:14244–14249

    CAS  PubMed Central  PubMed  Google Scholar 

  • Clifton SW, Minx P, Fauron CM et al (2004) Sequence and comparative analysis of the maize NB mitochondrial genome. Plant Physiol 136:3486–3503

    CAS  PubMed Central  PubMed  Google Scholar 

  • Conklin PL, Hanson MR (1994) Recombination of plant mitochondrial genomes. In: Paszkowski (ed) Homologous recombination and gene silencing in plants. Springer, Dordrecht, pp 61–81

    Google Scholar 

  • Correns C (1909) Zeit. Vererbungsl 1:291–329

    Google Scholar 

  • Corriveau JL, Coleman AW (1988) Rapid screening method to detect potential biparental inheritance of plastid DNA and results for over 200 angiosperm species. Am J Bot 75(10):1443–1458

    Google Scholar 

  • Daley DO, Whelan J (2005) Why genes persist in organelle genomes. Genome Biol 6(5):11

    Google Scholar 

  • Daniell H, Lee SB, Grevich J, Saski C et al (2006) Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes. Theor Appl Genet 112(8):1503–1518

    CAS  PubMed  Google Scholar 

  • Dasmahapatra KK, Mallet J (2006) DNA barcodes: recent successes and future prospects. Heredity 97:254–255

    CAS  PubMed  Google Scholar 

  • Davis CC, Wurdack KJ (2004) Host-to-parasite gene transfer in flowering plants: phylogenetic evidence from Malpighiales. Science 305:676–678

    CAS  PubMed  Google Scholar 

  • de Grey ADNJ (2005) Forces maintaining organellar genomes: is any as strong as genetic code disparity or hydrophobicity? Bioessays 27:436–446

    PubMed  Google Scholar 

  • Dombrowski S, Hoffmann M, Kuhn J, Brennick A, Binder S (1998) On mitochondrial promoters in Arabidopsis thaliana and other flowering plants. In: Möller IM, Glaser E, Glimelius K (eds) Plant mitochondria. Backhuys Publishers, Leiden, pp 165–170

    Google Scholar 

  • Douglas SE (1998) Plastid evolution: origins, diversity, trends. Curr Opin Genet Dev 8(6):655–661

    CAS  PubMed  Google Scholar 

  • Duchêne AM, Pujol C, Maréchal-Drouard L (2009) Import of tRNAs and aminoacyl-tRNA synthetases into mitochondria. Curr Genet 55(1):1–18

    PubMed  Google Scholar 

  • Ellis J (1982) Promiscuous DNA—chloroplast genes inside plant mitochondria. Nature 299:678–679

    CAS  PubMed  Google Scholar 

  • Erickson L, Kemble R (1990) Paternal inheritance of mitochondria in rapeseed (Brassica napus). Mol Gen Genet 222(1):135–139

    CAS  PubMed  Google Scholar 

  • Fairbanks DJ, Smith SE, Brown JK (1988) Inheritance of large mitochondrial RNAs in alfalfa. Theor Appl Genet 76(4):619–622

    CAS  PubMed  Google Scholar 

  • Farrelly F, Butow RA (1983) Rearranged mitochondrial genes in the yeast nuclear genome. Nature 301:296–301

    CAS  PubMed  Google Scholar 

  • Faure S, Noyer JL, Carreel F, Horry JP, Bakry F, Lanaud C (1994) Maternal inheritance of chloroplast genome and paternal inheritance of mitochondrial genome in bananas (Musa acuminata). Curr Genet 25(3):265–269

    CAS  PubMed  Google Scholar 

  • Fauron C, Casper M, Gao Y, Moore B (1995) The maize mitochondrial genome: dynamic yet functional. Trends Genet 11(6):228–235

    CAS  PubMed  Google Scholar 

  • Fojtová M, Kovarik A, Matyásek R (2001) Cytosine methylation of plastid genome in higher plants. Fact or artefact? Plant Sci 160:585–593

    PubMed  Google Scholar 

  • Gabay-Laughnan S, Newton KJ (2012) Plant mitochondrial mutations. In: Bock R, Knoop V (eds) Genomics of chloroplasts and mitochondria. Springer, Berlin, pp 175–200

    Google Scholar 

  • Gauly A, Kossel H (1989) Evidence for tissue-specific cytosine-methylation of plastid DNA from Zea mays. Curr Genet 15:371–376

    CAS  Google Scholar 

  • Gellissen G, Bradfield JY, White BN, Wyatt GR (1983) Mitochondrial DNA sequences in the nuclear genome of locust. Nature 301:631–634

    CAS  PubMed  Google Scholar 

  • Gray MW (1999) Evolution of organellar genomes. Curr Opin Genet Dev 9:678–687

    CAS  PubMed  Google Scholar 

  • Gray MW, Archibald JM (2012) Origins of mitochondria and plastids. In: Bock R, Knoop V (eds) Advances in photosynthesis and respiration. Springer, Berlin, pp 1–30

    Google Scholar 

  • Hagemann R (2010) The foundation of extranuclear inheritance: plastid and mitochondrial genetics. Mol Genet Genomics 283:199–209

    CAS  PubMed  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. Nucl Acids Res 31(20):5907–5916

    CAS  PubMed Central  PubMed  Google Scholar 

  • Hansen AK, Escobar LK, Gilbert LE, Jansen RK (2007) Paternal, maternal, and biparental inheritance of the chloroplast genome in Passiflora (Passifloraceae): implications for phylogenetic studies. Am J Bot 94(1):42–46

    CAS  PubMed  Google Scholar 

  • Hansmann P, Falk H, Ronai K, Sitte P (1985) Structure, composition, and distribution of plastid nucleoids in Narcissus pseudonarcissus. Planta 164:459–472

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed Central  PubMed  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 U S A 106(39):16728–16733

    CAS  PubMed Central  PubMed  Google Scholar 

  • Havey MJ (1997) Predominant paternal transmission of the mitochondrial genome in cucumber. J Hered 88(3):232–235

    Google Scholar 

  • Hebert PDN, Cywinska A, Ball SL, deWaard JR (2003) Biological identifications through DNA barcodes. Proc R Soc Biol Sci Ser B 270:313–321

    CAS  Google Scholar 

  • Henze K, Martin W (2001) How do mitochondrial genes get into the nucleus? Trends Genet 17(7):383–387

    CAS  PubMed  Google Scholar 

  • Hilu KW, Liang H (1997) The matK gene: sequence variation and application in plant systematics. Am J Bot 84:830–839

    CAS  PubMed  Google Scholar 

  • Hollingsworth PM, Graham SW, Little DP (2011) Choosing and using a plant DNA barcode. PLoS One 6(5):e19254

    CAS  PubMed Central  PubMed  Google Scholar 

  • Howe CJ, Smith AG (1991) Plants without chlorophyll. Nature 349:109

    Google Scholar 

  • Huang CY, Ayliffe MA, Timmis JN (2003) Direct measurement of the transfer rate of chloroplast DNA into the nucleus. Nature 422:72–76

    CAS  PubMed  Google Scholar 

  • Huang CY, Gru¨nheit N, Ahmadinejad N, Timmis JN, Martin W (2005) Mutational decay and age of chloroplast and mitochondrial genomes transferred recently to angiosperm nuclear chromosomes. Plant Physiol 138:1723–1733

    CAS  PubMed Central  PubMed  Google Scholar 

  • Jaffé B, Kovács K, Andras C, Bódi Z, Liu Z, Fray RG (2008) Methylation of chloroplast DNA does not affect viability and maternal inheritance in tobacco and may provide a strategy towards transgene containment. Plant Cell Rep 27:1377–1384

    PubMed Central  PubMed  Google Scholar 

  • Jobson RW, Qiu Y (2008) Did RNA editing in plant organellar genomes originate under natural selection or through genetic drift? Biol Direct 3:43

    PubMed Central  PubMed  Google Scholar 

  • Kitazaki K, Kubo T (2010) Cost of having the largest mitochondrial genome: evolutionary mechanism of plant mitochondrial genome. J Bot 620137:1–12

    Google Scholar 

  • Kmiec B, Woloszynska M, Janska H (2006) Heteroplasmy as a common state of mitochondrial genetic information in plants and animals. Curr Genet 50:149–159

    CAS  PubMed  Google Scholar 

  • Knoop V (2004) The mitochondrial DNA of land plants: peculiarities in phylogenetic perspective. Curr Genet 46:123–139

    CAS  PubMed  Google Scholar 

  • Knoop V (2012) Seed plant mitochondrial genomes: complexity evolving. In: Bock R, Knoop V (eds) Genomics of chloroplasts and mitochondria. Springer, Dordrecht, pp 175–200

    Google Scholar 

  • Knoop V, Ehrhardt T, Lattig K, Brennicke A (1995) The gene for ribosomal protein S10 is present in mitochondria of pea and potato but is absent from those of Arabidopsis and Oenothera. Curr Genet 27:559–564

    CAS  PubMed  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

    CAS  PubMed Central  PubMed  Google Scholar 

  • Kobayashi H, Ngernprasirtsiri J, Akazawa T (1990) Transcriptional regulation and DNA methylation in plastids during transitional conversion of chloroplasts to chromoplasts. EMBO J 9:307–313

    CAS  PubMed Central  PubMed  Google Scholar 

  • Krupinska K, Melonek J, Krause K (2013) New insights into plastid nucleoid structure and functionality. Planta 237:653–664

    CAS  PubMed  Google Scholar 

  • Kubo T, Mikami T (2007) Organization and variation of angiosperm mitochondrial genome. Physiol Plant 129:6–13

    CAS  Google Scholar 

  • Kubo T, Newton KJ (2008) Angiosperm mitochondrial genomes and mutations. Mitochondrion 8(1):5–14

    CAS  PubMed  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(13):2571–2576

    CAS  PubMed Central  PubMed  Google Scholar 

  • Kumar AM, Schaub U, Soll D, Ujwal ML (1996) Glutamyl-transfer RNA: at the crossroad between chlorophyll and protein biosynthesis. Trends Plant Sci 1(11):371–376

    Google Scholar 

  • Kuroiwa T (1991) The replication, differentiation, and inheritance of plastids with emphasis on the concept of organelle nuclei. Int Rev Cytol 128:1–62

    CAS  Google Scholar 

  • Lambowitz AM, Zimmerly S (2004) Mobile group II introns. Annu Rev Genet 38:1–35

    CAS  PubMed  Google Scholar 

  • Leister D (2005) Origin, evolution and genetic effects of nuclear insertions of organelle DNA. Trends Genet 21(12):655–663

    CAS  PubMed  Google Scholar 

  • Li X, Yang Y, Henry RJ, Rosset M, Wang Y, Chen S (2015) Plant DNA barcoding: from gene to genome. Biol Rev 90(1):157–166

    Google Scholar 

  • Lilly JW, Havey MJ, Jackson SA, Jiang J (2001) Cytogenomic analyses reveal the structural plasticity of the chloroplast genome in higher plants. Plant Cell 13:245–254

    CAS  PubMed Central  PubMed  Google Scholar 

  • Linneweber CS, Small I (2008) Pentatricopeptide repeat proteins: a socket set for organelle gene expression. Trends Plant Sci 13(12):663–670

    Google Scholar 

  • Liu Y, Zhang Q, Hu Y, Sodmergen (2004) Heterogeneous pollen in Chlorophytum comosum, a species with a unique mode of plastid inheritance intermediate between the maternal and biparental modes. Plant Physiol 135:193–200

    CAS  PubMed Central  PubMed  Google Scholar 

  • Lloyd AH, Timmis JN (2011) The origin and characterization of new nuclear genes originating from a cytoplasmic organellar. Genome Mol Biol Evol 28(7):2019–2028

    CAS  Google Scholar 

  • Lloyd AH, Rousseau-Gueutin M, Sheppard AE, Ayliffe MA, Timmis JN (2012) Promiscuous organellar DNA. In: Bock R, Knoop V (eds) Advances in photosynthesis and respiration. Springer, Berlin, pp 201–221

    Google Scholar 

  • Lonsdale DM, Hodge TP, Fauron CMR (1984) The physical map and organization of the mitochondrial genome from the fertile cytoplasm of maize. Nucl Acids Res 12(24):9249–9261

    CAS  PubMed Central  PubMed  Google Scholar 

  • Lynch M (1996) Mutation accumulation in transfer rnas: molecular evidence for Muller’s ratchet in mitochondrial genomes. Mol Biol Evol 13(1):209–220

    CAS  PubMed  Google Scholar 

  • Majeran W, Friso G, Asakura Y, Qu X, Huang M, Ponnala L, Watkins KP, Barkan A, van Wijk KJ (2012) Nucleoid-enriched proteomes in developing plastids and chloroplasts from maize leaves: a new conceptual framework for nucleoid functions. Plant Physiol 158:156–189

    CAS  PubMed Central  PubMed  Google Scholar 

  • Marano MR, Carrillo N (1991) Chromoplast formation during tomato fruit ripening. No evidence for plastid methylation. Plant Mol Biol 16:11–19

    CAS  PubMed  Google Scholar 

  • Maréchal-Drouard L, Weil JH, Dietrich A (1993) Transfer RNAs and transfer RNA genes in plants. Annu Rev Plant Physiol 44:13–32

    Google Scholar 

  • Margulis L (1970) Origin of eukaryotic cells. Yale University Press, New Haven, p 349

    Google Scholar 

  • Marienfeld J, Unseld M, Brennicke A (1999) The mitochondrial genome of Arabidopsis is composed of both native and immigrant information. Trends Plant Sci 4:495–502

    PubMed  Google Scholar 

  • Martin W (2003) Gene transfer from organelles to the nucleus: frequent and in big chunks. Proc Natl Acad Sci U S A 100:8612–8614

    CAS  PubMed Central  PubMed  Google Scholar 

  • Martin W, Kowallik KV (1999) Annotated English translation of Mereschkowsky’s 1905 paper “Über Natur und Ursprung der Chromatophoren im Pflanzenreiche.’. Eur J Phycol 34:287–295

    Google Scholar 

  • Martin W, Rujan T, Richly E, Hansen A, Cornelsen S, Lins T, Leister D, Stoebe B, Hasegawa M, Penny D (2002) Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc Natl Acad Sci U S A 99:12246–12251

    CAS  PubMed Central  PubMed  Google Scholar 

  • Matsuo M, Ito Y, Yamauchi R, Obokata J (2005) The rice nuclear genome continuously integrates, shuffles, and eliminates the chloroplast genome to cause chloroplast–nuclear DNA flux. Plant Cell 17:665–675

    CAS  PubMed Central  PubMed  Google Scholar 

  • McCauley DE (2013) Paternal leakage, heteroplasmy, and the evolution of plant mitochondrial genomes. New Phytol 200(4):966–977

    PubMed  Google Scholar 

  • Melonek J, Matros A, Trösch M, Mock HP, Krupinska K (2012) The core of chloroplast nucleoids contains architectural SWIB domain proteins. Plant Cell 24(7):3060–3073

    CAS  PubMed Central  PubMed  Google Scholar 

  • Mereschkowski C (1905) Über Natur und Ursprung der Chromatophoren im Pflanzenreiche. Biol Centralbl 25:593–604 [English translation (1999) Eur J Phycol 34:287–295]

    Google Scholar 

  • Miyamura S, Nagata T, Kuroiwa T (1986) Quantitative fluorescence microscopy on dynamic changes of plastid nucleoids during wheat development. Protoplasma 133:66–72

    CAS  Google Scholar 

  • Miyata S, Nakazono M, Hirai A (1998) Transcription of plastid-derived tRNA genes in rice mitochondria. Curr Genet 34(3):216–220

    CAS  PubMed  Google Scholar 

  • Moran NA (2002) Microbial minimalism: genome reduction in bacterial pathogens. Cell 108:583–586

    CAS  PubMed  Google Scholar 

  • Mower JP, Stefanović S, Young GJ, Palmer JD (2004) Plant genetics: gene transfer from parasitic to host plants. Nature 432:165–166

    CAS  PubMed  Google Scholar 

  • Mower JP, Stefanovic S, Gummow JS, Hao W, 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 (1–16)

    CAS  PubMed Central  PubMed  Google Scholar 

  • Mower JP, Case AL, Floro ER, Willis JH (2012) Evidence against equimolarity of large repeat arrangements and a predominant master circle structure of the mitochondrial genome from a monkeyflower (Mimulus guttatus) lineage with cryptic CMS. Genome Biol Evol 4(5):670–686

    PubMed Central  PubMed  Google Scholar 

  • Nagata (2010) Mechanisms for independent cytoplasmic inheritance of mitochondria and plastids in angiosperms. J Plant Res 123:193–199

    PubMed  Google Scholar 

  • Neale DB, Marshall KA, Sederoff RR (1989) Chloroplast and mitochondrial DNA are paternally inherited in Sequoia sempervirens D. Don Endl. Proc Natl Acad Sci U S A 86:9347–9349

    CAS  PubMed Central  PubMed  Google Scholar 

  • Ngernprasirtsiri J, Kobayashi H, Akazawa T (1988a) DNA methylation occurred around lowly expressed genes of plastid DNA during tomato fruit development. Plant Physiol 88:16–20

    CAS  PubMed Central  PubMed  Google Scholar 

  • Ngernprasirtsiri J, Kobayashi H, Akazawa T (1988b) DNA methylation as a mechanism of transcriptional regulation in nonphotosynthetic plastids in plant cells. Proc Natl Acad Sci U S A 85:4750–4754

    CAS  PubMed Central  PubMed  Google Scholar 

  • Ngernprasirtsiri J, Chollet RST, Kobayashill H, Sugiyama T, Akazawa T (1989) DNA methylation and the differential expression of C4 photosynthesis genes in mesophyll and bundle sheath cells of greening maize leaves. J Biol Chem 264(14):8241–8248

    CAS  PubMed  Google Scholar 

  • Nickrent DL, Ouyang Y, Duff RJ, dePamphilis CW (1997) Do nonasterid holoparasitic flowering plants have plastid genomes? Plant Mol Biol 34:717–729

    CAS  PubMed  Google Scholar 

  • Nishiyama R, Ito M, Yamaguchi Y, Koizumi N, Sano H (2002) A chloroplast-resident DNA methyltransferase is responsible for hypermethylation of chloroplast genes in Chlamydomonas maternal gametes. Proc Natl Acad Sci U S A 99:5925–5930

    CAS  PubMed Central  PubMed  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

    CAS  PubMed  Google Scholar 

  • Noutsos C, Richly E, Leister D (2005) Generation and evolutionary fate of insertions of organelle DNA in the nuclear genomes of flowering plants. Genome Res 15:616–628

    CAS  PubMed Central  PubMed  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

    CAS  PubMed  Google Scholar 

  • Oca-Cossio J, Kenyon L, Hao H, Moraes CT (2003) Limitations of allotropic expression of mitochondrial genes in mammalian cells. Genetics 165:707–720

    CAS  PubMed Central  PubMed  Google Scholar 

  • Ogihara Y, Yamazaki Y, Murai K, Kanno A et al (2005) Structural dynamics of cereal mitochondrial genomes as revealed by complete nucleotide sequencing of the wheat mitochondrial genome. Nucl Acids Res 33:6235–6250

    CAS  PubMed Central  PubMed  Google Scholar 

  • Ohta N, Sato N, Kawano S, Kuroiwa T (1991) Methylation of DNA in the chloroplasts and amyloplasts of the pea, Pisum sativum. Plant Sci 78:33–42

    CAS  Google Scholar 

  • Ohyama K, Fukuzawa H, Kohchi T, Shirai H, Sano T, Sano S, Umesono K, Shiki Y, Takeuchi M, Chang Z, Aota SI, Inokuchi H, Ozeki H (1986) Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA. Nature 322:572–574

    CAS  Google Scholar 

  • Palmer JD (1983) Chloroplast DNA exists in two orientations. Nature 301:92–93

    CAS  Google Scholar 

  • Palmer JD (1985) Comparative organization of chloroplast genomes. Annu Rev Genet 19:325–354

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

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

    CAS  Google Scholar 

  • Palmer JD, Adams KL, Cho Y, Parkinson CL, Song K (2000) Dynamic evolution of plant mitochondrial genomes: mobile genes and introns and highly variable mutation rates. Proc Natl Acad Sci U S A 97:6960–6966

    CAS  PubMed Central  PubMed  Google Scholar 

  • Palmgren G, Mattsson O, Okkels FT (1991) Specific levels of DNA methylation in various tissues, cell lines, and cell types of Daucus carota. Plant Physiol 95:174–178

    CAS  PubMed Central  PubMed  Google Scholar 

  • Pennisi E (2007) Wanted: a barcode for plants. Science 318:190–191

    CAS  PubMed  Google Scholar 

  • Pfalz J, Liere K, Kandlbinder A, Dietz K-J, Oelmu¨ller R (2006) pTAC2, -6, and -12 are components of the transcriptionally active plastid chromosome that are required for plastid gene expression. Plant Cell 18:176–197

    CAS  PubMed Central  PubMed  Google Scholar 

  • Pfannschmidt T, Schutze K, Fey V, Sherameti I, Oelmuller R (2003) Chloroplast redox control of nuclear gene expression – a new class of plastid signals in interorganellar communication. Antioxid Redox Signal 5:95–101

    CAS  PubMed  Google Scholar 

  • Phinney BS, Thelen JJ (2005) Proteomic characterization of a Triton insoluble fraction from chloroplasts defines a novel group of proteins associated with macromolecular structures. J Proteome Res 4:497–506

    CAS  PubMed  Google Scholar 

  • Ravi V, Khurana JP, Tyagi AK, Khurana P (2008) An update on chloroplast genomes. Plant Syst Evol 271:101–122

    CAS  Google Scholar 

  • Richly E, Leister D (2004a) NUMTs in sequenced eukaryotic genomes. Mol Biol Evol 21:1081–1084

    CAS  PubMed  Google Scholar 

  • Richly E, Leister D (2004b) NUPTs in sequenced eukaryotes and their genomic organization in relation to NUMTs. Mol Biol Evol 21:1972–1980

    CAS  PubMed  Google Scholar 

  • Sager R, Grabowy C (1983) Differential methylation of chloroplast DNA regulates maternal inheritance in a methylated mutant of Chlamydomonas. Proc Natl Acad Sci U S A 80:3025–3029

    CAS  PubMed Central  PubMed  Google Scholar 

  • Sager R, Lane D (1972) Molecular basis of maternal inheritance. Proc Natl Acad Sci U S A 69(9):2410–2413

    CAS  PubMed Central  PubMed  Google Scholar 

  • Sakai A, Takano H, Kuroiwa T (2004) Organelle nuclei in higher plants: structure, composition, function, and evolution. Int Rev Cytol 238:59–118

    CAS  PubMed  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(8):1762–1777

    CAS  PubMed Central  PubMed  Google Scholar 

  • Sato N, Terasawa K, Miyajima K, Kabeya Y (2003) Organization, developmental dynamics, and evolution of plastid nucleoids. Int Rev Cytol 232:217–262

    CAS  PubMed  Google Scholar 

  • Schardl CL, Lonsdale DM, Pring DR, Rose KR (1984) Linearization of maize mitochondrial chromosomes by recombination with linear episomes. Nature 310:292–296

    CAS  Google Scholar 

  • Schljster 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

    Google Scholar 

  • Selosse MA, Albert B, Godelle B (2001) Reducing the genome size of organelles favours gene transfer to the nucleus. Trends Ecol Evol 16(3):135–141

    PubMed  Google Scholar 

  • Shearman JR, Sangsrakru D, Ruang-areerate P, Sonthirod C, Uthaipaisanwong P et al (2014) Assembly and analysis of a male sterile rubber tree mitochondrial genome reveals DNA rearrangement events and a novel transcript. BMC Plant Biol 14:45

    PubMed Central  PubMed  Google Scholar 

  • Shinozaki K, Ohme M, Tanaka M, Wakasugi T et al (1986) The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J 5(9):2043–2049

    CAS  PubMed Central  PubMed  Google Scholar 

  • Shore JS, McQueen KL, Little SH (1994) Inheritance of plastid DNA in the Turnera ulmifolia complex (Turneraceae). Am J Bot 81:1636–1639

    Google Scholar 

  • Sloan DB (2013) One ring to rule them all? Genome sequencing provides new insights into the ‘master circle’ model of plant mitochondrial DNA structure. New Phytol 200(4):978–985

    CAS  PubMed  Google Scholar 

  • Stegemann S, Bock R (2006) Experimental reconstruction of functional gene transfer from the tobacco plastid genome to the nucleus. Plant Cell 18:2869–2878

    CAS  PubMed Central  PubMed  Google Scholar 

  • Stegemann S, Hartmann S, Ruf S, Bock R (2003) High-frequency gene transfer from the chloroplast genome to the nucleus. Proc Natl Acad Sci U S A 100(15):8828–8833

    CAS  PubMed Central  PubMed  Google Scholar 

  • Steiner S, Schro¨ter Y, Pfalz J, Pfannschmidt T (2011) Identification of essential subunits in the plastid-encoded RNA polymerase complex reveals building blocks for proper plastid development. Plant Physiol 157:1043–1055

    CAS  PubMed Central  PubMed  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

    CAS  PubMed  Google Scholar 

  • Stupar RM, Lilly JW, Town CD, Cheng Z, Kaul S, Buell CR, Jiang J (2001) Complex mtDNA constitutes an approximate 620-kb insertion on Arabidopsis thaliana chromosome 2: implication of potential sequencing errors caused by large-unit repeats. Proc Natl Acad Sci U S A 98:5099–5103

    CAS  PubMed Central  PubMed  Google Scholar 

  • Sugita M, Sugiura M (1996) Regulation of gene expression in chloroplasts of higher plants. Plant Mol Biol 32(1–2):315–326

    CAS  PubMed  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(6):603–615

    CAS  PubMed  Google Scholar 

  • Suzuki MM, Bird A (2008) DNA methylation landscapes: provocative insights from epigenomics. Nat Rev Genet 9(6):465–476

    CAS  PubMed  Google Scholar 

  • Testolin R, Cipriani G (1997) Paternal inheritance of chloroplast DNA and maternal inheritance of mitochondrial DNA in the genus Actinidia. Theor Appl Genet 94:897–903

    CAS  Google Scholar 

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

    CAS  PubMed Central  PubMed  Google Scholar 

  • Tomas R, Vera A, Martin M, Sabater B (1992) Changes in protein synthesis without evidence of DNA methylation in barley chloroplasts during leaf growth and development. Plant Sci 85:71–77

    CAS  Google Scholar 

  • Umen JG, Goodenough UW (2001) Chloroplast DNA methylation and inheritance in Chlamydomonas. Genes Dev 15:2585–2597

    CAS  PubMed Central  PubMed  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 1:57–61

    Google Scholar 

  • van den Boogaart P, Samallo J, Agsteribbe E (1982) Similar genes for a mitochondrial ATPase subunit in the nuclear and mitochondrial genomes of Neurospora crassa. Nature 298:187–189

    PubMed  Google Scholar 

  • VanWinkle-Swift KP (1980) A model for the rapid vegetative segregation of multiple chloroplast genomes in Chlamydomonas: assumptions and predictions of the model. Curr Genet 1:113–125

    CAS  PubMed  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(5):563–572

    CAS  PubMed  Google Scholar 

  • Von Heijne G (1986) Why mitochondria need a genome. FEBS Lett 198:1–4

    Google Scholar 

  • Wang D, Wu YW, Shih AC, Wu CS, Wang YN, Chaw SM (2007) Transfer of chloroplast genomic DNA to mitochondrial genome occurred at least 300 MYA. Mol Biol Evol 24:2040–2048

    CAS  PubMed  Google Scholar 

  • Wang D, Rousseau-Gueutin M, Timmis JN (2012a) Plastid sequences contribute to some plant mitochondrial genes. Mol Biol Evol 29(7):1707–1711

    CAS  PubMed  Google Scholar 

  • Wang D, Lloyd AH, Timmis JN (2012b) Environmental stress increases the entry of cytoplasmic organellar DNA into the nucleus in plants. Proc Natl Acad Sci U S A 109(7):2444–2448

    CAS  PubMed Central  PubMed  Google Scholar 

  • Ward B, Anderson R, Bendich A (1981) The size of the mitochondrial genome is large and variable in a family of plants (Cucurbitaceae). Cell 25:793–803

    CAS  PubMed  Google Scholar 

  • Weihe A, Apitz J, Pohlheim F, Salinas-Hartwig A, Börner T (2009) Biparental inheritance of plastidial and mitochondrial DNA and hybrid variegation in Pelargonium. Mol Genet Genomics 282(6):587–593

    CAS  PubMed Central  PubMed  Google Scholar 

  • Wells WA (2005) There’s DNA in those organelles. J Cell Biol 168(6):853–856

    CAS  PubMed Central  Google Scholar 

  • Wilson RJM (2005) Parasite plastids: approaching the endgame. Biol Rev Camb Philos Soc 80:129–153

    PubMed  Google Scholar 

  • Wolfe KH, Mordent CW, Palmer JD (1992) Function and evolution of a minimal plastid genome from a nonphotosynthetic parasitic plant. Proc Natl Acad Sci U S A 89:10648–10652

    CAS  PubMed Central  PubMed  Google Scholar 

  • Woloszynska M, Bocer T, Mackiewicz P, Janska H (2004) A fragment of chloroplast DNA was transferred horizontally, probably from non-eudicots, to mitochondrial genome of Phaseolus. Plant Mol Biol 56(5):811–820

    CAS  PubMed  Google Scholar 

  • Wright RM, Cummings DJ (1983) Integration of mitochondrial gene sequences within the nuclear genome during senescence in a fungus. Nature 302:86–88

    CAS  PubMed  Google Scholar 

  • Xi Z, Wang Y, Bradley RK, Sugumaran M, Marx CJ, Joshua SR, Charles CD (2013) Massive mitochondrial gene transfer in a parasitic flowering plant clade. PLoS Genet 9(2):e1003265

    CAS  PubMed Central  PubMed  Google Scholar 

  • Yagi Y, Shiina T (2014) Recent advances in the study of chloroplast gene expression and its evolution. Front Plant Sci 5:61–84

    PubMed Central  PubMed  Google Scholar 

  • Yang TW, Yang YA, Xiong Z (2000) Paternal inheritance of chloroplast DNA in interspecific hybrids in the genus Larrea (Zygophyllaceae). Am J Bot 87(10):1452–1458

    CAS  PubMed  Google Scholar 

  • Yu J, Xue JH, Zhou SL (2011) New universal matK primers for DNA barcoding angiosperms. J Syst Evol 49(3):176–181

    Google Scholar 

  • Zhang Q, Sodmergen (2010) Why does biparental plastid inheritance revive in angiosperms? J Plant Res 123:201–206

    PubMed  Google Scholar 

  • Zhang TW, Zhang XW, Hu SN, Yu J (2011) An efficient procedure for plant organellar genome assembly, based on whole genome data from the 454 GS FLX sequencing platform. Plant Methods 7:38–46

    CAS  PubMed Central  PubMed  Google Scholar 

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Acknowledgements

We thank the University Grants Commission, New Delhi, for Special Assistance Programme and Department of Science and Technology, New Delhi, for FIST and DU-DST PURSE programme. Senior Research Fellowship to Ami Choubey by the Council of Scientific and Industrial Research, New Delhi, is acknowledged.

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Correspondence to Manchikatla Venkat Rajam .

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Choubey, A., Rajam, M.V. (2015). Organellar Genomes of Flowering Plants. In: Bahadur, B., Venkat Rajam, M., Sahijram, L., Krishnamurthy, K. (eds) Plant Biology and Biotechnology. Springer, New Delhi. https://doi.org/10.1007/978-81-322-2283-5_8

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