Abstract
This chapter summarizes the main features of the tomato plastid and mitochondrial genomes in the context of the current knowledge about “orthologue” genomes from other higher plants species in a historical perspective. We have focused on the application of this knowledge to aid in deciphering the functional roles of these organelles in growth and developmental processes of the tomato plants, especially on those related to fruit ripening. It also presents an assessment of the phylogenetic position of tomato, based on the available information of plastid and chondrome sequences from other land plants; which adds to the understanding of the evolutionary history of plants.
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References
Abdelnoor RV, Yule R, Elo A et al (2003) Substoichiometric shifting in the plant mitochondrial genome is influenced by a gene homologous to MutS. Proc Natl Acad Sci USA 100:5968–5973. doi:10.1073/pnas.1037651100
Adachi J, Waddell PJ, Martin W, Hasegawa M (2000) Plastid genome phylogeny and a model of amino acid substitution for proteins encoded by chloroplast DNA. J Mol Evol 50:348–358. doi:10.1007/s002399910038
Adams K, Palmer J (2003) Evolution of mitochondrial gene content: gene loss and transfer to the nucleus. Mol Phylogenet Evol 29:380–395. doi:10.1016/S1055-7903(03)00194-5
Adams KL, Daley DO, Qiu YL et al (2000) Repeated, recent and diverse transfers of a mitochondrial gene to the nucleus in flowering plants. Nature 408:354–357. doi:10.1038/35042567
Allison LA, Simon LD, Maliga P (1996) Deletion of rpoB reveals a second distinct transcription system in plastids of higher plants. EMBO J 15:2802–2809
Alverson AJ, Wei X, Rice DW et al (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. doi:10.1093/molbev/msq029
Alverson AJ, Rice DW, Dickinson S et al (2011a) Origins and recombination of the bacterial-sized multichromosomal mitochondrial genome of cucumber. Plant Cell. doi:10.1105/tpc.111.087189
Alverson AJ, Zhuo S, Rice DW et al (2011b) The mitochondrial genome of the legume Vigna radiata and the analysis of recombination across short mitochondrial repeats. PLoS One 6:e16404
Anderson S, Bankier A, Barrell B et al (1981) Sequence and organization of the human mitochondrial genome. Nature 290:457–465
Arrieta-Montiel M, Lyznik A, Woloszynska M et al (2001) Tracing evolutionary and developmental implications of mitochondrial stoichiometric shifting in the common bean. Genetics 158:851–864
Asano T, Tsudzuki T, Takahashi S et al (2004) Complete nucleotide sequence of the sugarcane (Saccharum officinarum) chloroplast genome: a comparative analysis of four monocot chloroplast genomes. DNA Res 11:93–99
Ayliffe MA, Timmis JN (1992a) Tobacco nuclear DNA contains long tracts of homology to chloroplast DNA. Theor Appl Genet 85–85:229–238. doi:10.1007/BF00222864
Ayliffe MA, Timmis JN (1992b) Plastid DNA sequence homologies in the tobacco nuclear genome. Mol Gen Genet 236:105–112
Ayliffe MA, Scott NS, Timmis JN (1998) Analysis of plastid DNA-like sequences within the nuclear genomes of higher plants. Mol Biol Evol 15:738–745
Backert S, Börner T (2000) Phage T4-like intermediates of DNA replication and recombination in the mitochondria of the higher plant Chenopodium album (L.). Curr Genet 37:304–314
Baldauf SL, Palmer JD (1990) Evolutionary transfer of the chloroplast tufA gene to the nucleus. Nature 344:262–265
Barkan A, Goldschmidt-Clermont M (2000) Participation of nuclear genes in chloroplast gene expression. Biochimie 82:559–572
Barsan C, Zouine M, Maza E et al (2012) Proteomic analysis of chloroplast-to-chromoplast transition in tomato reveals metabolic shifts coupled with disrupted thylakoid biogenesis machinery and elevated energy-production components. Plant Physiol 160:708–725. doi:10.1104/pp.112.203679
Bathgate B, Purton ME, Grierson D, Goodenough PW (1985) Plastid changes during the conversion of chloroplasts to chromoplasts in ripening tomatoes. Planta 165:197–204. doi:10.1007/BF00395042
Bausher MG, Singh ND, Lee S-B et al (2006) The complete chloroplast genome sequence of Citrus sinensis (L.) Osbeck var “Ridge Pineapple”: organization and phylogenetic relationships to other angiosperms. BMC Plant Biol 6:21. doi:10.1186/1471-2229-6-21
Bedbrook JR, Bogorad L (1976) Endonuclease recognition sites mapped on Zea mays chloroplast DNA. Proc Natl Acad Sci USA 73:4309–4313
Bedbrook JR, Kolodner R, Bogorad L (1977) Zea mays chloroplast ribosomal RNA genes are part of a 22,000 base pair inverted repeat. Cell 11:739–749
Bendich AJ (2004) Circular chloroplast chromosomes: the grand illusion. Plant Cell 16:1661–1666. doi:10.1105/tpc.160771
Bensasson D, Zhang D-X, Hartl DL, Hewitt GM (2001) Mitochondrial pseudogenes: evolution’s misplaced witnesses. Trends Ecol Evol 16:314–321. doi:10.1016/S0169-5347(01)02151-6
Blanehard JL, Schmidt GW (1995) Pervasive migration of organellar DNA to the nucleus in plants. J Mol Evol 41:397–406
Bock R (2000) Sense from nonsense: how the genetic information of chloroplasts is altered by RNA editing. Biochimie 82:549–557
Cai Z, Penaflor C, Kuehl JV et al (2006) Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogenetic relationships of magnoliids. BMC Evol Biol 6:77. doi:10.1186/1471-2148-6-77
Chang C-C, Lin H-C, Lin I-P et al (2006) The chloroplast genome of Phalaenopsis aphrodite (Orchidaceae): comparative analysis of evolutionary rate with that of grasses and its phylogenetic implications. Mol Biol Evol 23:279–291. doi:10.1093/molbev/msj029
Chaw S-M, Shih AC-C, Wang D et al (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. doi:10.1093/molbev/msn009
Chen J, Guan R, Chang S et al (2011) Substoichiometrically different mitotypes coexist in mitochondrial genomes of Brassica napus L. PLoS One 6:e17662
Cheung WY, Scott NS (1989) A contiguous sequence in spinach nuclear DNA is homologous to three separated sequences in chloroplast DNA. Theor Appl Genet 77:625–633
Chumley TW, Palmer JD, Mower JP et al (2006) The complete chloroplast genome sequence of Pelargonium × hortorum: organization and evolution of the largest and most highly rearranged chloroplast genome of land plants. Mol Biol Evol 23:2175–2190. doi:10.1093/molbev/msl089
Chung H-J, Jung JD, Park H-W et al (2006) The complete chloroplast genome sequences of Solanum tuberosum and comparative analysis with Solanaceae species identified the presence of a 241-bp deletion in cultivated potato chloroplast DNA sequence. Plant Cell Rep 25:1369–1379. doi:10.1007/s00299-006-0196-4
Clarkson JJ, Knapp S, Garcia VF et al (2004) Phylogenetic relationships in Nicotiana (Solanaceae) inferred from multiple plastid DNA regions. Mol Phylogenet Evol 33:75–90. doi:10.1016/j.ympev.2004.05.002
Clifton SW, Minx P, Fauron CM et al (2004) Sequence and comparative analysis of the maize NB mitochondrial genome. Plant Physiol 136:3486–3503. doi:10.1104/pp.104.044602.3486
Conrad M (1985) The mutation buffering concept of biomolecular structure. J Biosci 8:669–679
Conte M, López M, Lichtenstein G, Carrari F (2013) Mitochondrial and ripening transcriptome analyses during tomato fruit development and ripening. In: 8th International Conference for Plant Mitochondrial Biology ICPMB 2013. Rosario, Argentina
Correns VCL (1908) Vererbungsversuche mit blass(gelb)grtinen und buntblittrigen Sippen bei Mirabilisjalapa, Urtica pilulifera und. Lunaria annua. Zeitschrift für Induktive Abstammungs und Vererbungslehre 1:291–329
Cui L, Veeraraghavan N, Richter A et al (2006) Chloroplast DB: the chloroplast genome database. Nucleic Acids Res 34:D692–D696. doi:10.1093/nar/gkj055
Daniell H, Lee S-B, Grevich J et al (2006) Complete chloroplast genome sequences of Solanum bulbocastanum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes. TAG Theor Appl Genet 112:1503–1518. doi:10.1007/s00122-006-0254-x
Darracq A, Varré J-S, Touzet P (2010) A scenario of mitochondrial genome evolution in maize based on rearrangement events. BMC Genom 11:233. doi:10.1186/1471-2164-11-233
De Las Rivas J, Lozano JJ, Ortiz AR (2002) Comparative analysis of chloroplast genomes: functional annotation, genome-based phylogeny, and deduced evolutionary patterns. Genome Res 12:567–583
Denovan-Wright EM, Nedelcu AM, Lee RW (1998) Complete sequence of the mitochondrial DNA of Chlamydomonas eugametos. Plant Mol Biol 36:285–295
Douglas SE, Penny SL (1999) The plastid genome of the cryptophyte alga, Guillardia theta: complete sequence and conserved synteny groups confirm its common ancestry with red algae. J Mol Evol 48:236–244
Du Jardin P (1990) Homologies to plastid DNA in the nuclear and mitochondrial genomes of potato. Theor Appl Genet 79:807–812. doi:10.1007/BF00224249
Eberhard S, Drapier D, Wollman F-A (2002) Searching limiting steps in the expression of chloroplast-encoded proteins: relations between gene copy number, transcription, transcript abundance and translation rate in the chloroplast of Chlamydomonas reinhardtii. Plant J Cell Mol Biol 31:149–160
Egea I, Bian W, Barsan C et al (2011) Chloroplast to chromoplast transition in tomato fruit: spectral confocal microscopy analyses of carotenoids and chlorophylls in isolated plastids and time-lapse recording on intact live tissue. Ann Bot 108:291–297. doi:10.1093/aob/mcr140
Fan J, Lee RW (2002) Mitochondrial genome of the colorless green alga Polytomella parva: two linear DNA molecules with homologous inverted repeat Termini. Mol Biol Evol 19:999–1007
Fauron C, Casper M (1995) The maize mitochondrial genome: dynamic, yet functional. Trends Genet TIG 11:228–235
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791
Fleischmann TT, Scharff LB, Alkatib S et al (2011) Nonessential plastid-encoded ribosomal proteins in tobacco: a developmental role for plastid translation and implications for reductive genome evolution. Plant Cell 23:3137–3155. doi:10.1105/tpc.111.088906
Gibor A, Granick S (1964) Plastids and mitochondria: inheritable systems: do plastids and mitochondria contain a chromosome which controls their multiplication and development? Science 145:890–897. doi:10.1126/science.145.3635.890
Goremykin VV, Hirsch-Ernst KI, Wolfl S, Hellwig FH (2003) Analysis of the Amborella trichopoda chloroplast genome sequence suggests that amborella is not a basal angiosperm. Mol Biol Evol 20:1499–1505. doi:10.1093/molbev/msg159
Goremykin VV, Holland B, Hirsch-Ernst KI, Hellwig FH (2005) Analysis of Acorus calamus chloroplast genome and its phylogenetic implications. Mol Biol Evol 22:1813–1822. doi:10.1093/molbev/msi173
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. doi:10.1093/molbev/msn226
Graham LE, Cook ME, Busse JS (2000) The origin of plants: body plan changes contributing to a major evolutionary radiation. Proc Natl Acad Sci USA 97:4535–4540
Gray MW (1999) Evolution of organellar genomes. Curr Opin Genet Dev 9:678–687
Gray RE, Law RHP, Devenish RJ, Nagley P (1996) Allotopic expression of mitochondrial ATP synthase genes in nucleus of Saccharomyces cerevisiae. In: Attardi GM, Chomyn A (eds) Mitochondrial biogenesis and genetics, part B. Academic Press, London, pp 369–389
Gualberto JM, Wintz H, Weil JH, Grienenberger JM (1988) The genes coding for subunit 3 of NADH dehydrogenase and for ribosomal protein S12 are present in the wheat and maize mitochondrial genomes and are co-transcribed. Mol Gen Genet MGG 215:118–127
Guilliermond A, Atkinson LMR (1941) The cytoplasm of the plant cell. In: Frans Verdoorn (ed) A new series of plant science books
Guo X, Castillo-Ramírez S, González V et al (2007) Rapid evolutionary change of common bean (Phaseolus vulgaris L.) plastome, and the genomic diversification of legume chloroplasts. BMC Genom 8:228. doi:10.1186/1471-2164-8-228
Hajdukiewicz PT, Allison LA, Maliga P (1997) The two RNA polymerases encoded by the nuclear and the plastid compartments transcribe distinct groups of genes in tobacco plastids. EMBO J 16:4041–4048. doi:10.1093/emboj/16.13.4041
Harris WM, Spurr AR (1969) Chromoplasts of tomato fruits. II. The red tomato. Am J Bot 56:380–389
Hazkani-Covo E, Zeller RM, Martin W (2010) Molecular poltergeists: mitochondrial DNA copies (numts) in sequenced nuclear genomes. PLoS Genet 6:e1000834. doi:10.1371/journal.pgen.1000834
Hiratsuka J, Shimada H, Whittier R, et al. (1989) The complete sequence of the rice (Oryza sativa) chloroplast genome: intermolecular recombination between distinct tRNA genes accounts for a major plastid DNA inversion during the evolution of the cereals. Mol Gen Genet 217(2–3):185–194
Huang X, Madan A (1999) CAP3: A DNA sequence assembly program. Genome Res 9:868–877
Ibrahim RIH, Azuma J-I, Sakamoto M (2006) Complete nucleotide sequence of the cotton (Gossypium barbadense L.) chloroplast genome with a comparative analysis of sequences among 9 dicot plants. Genes Genet Syst 81:311–321
Iorizzo M, Senalik D, Szklarczyk M et al (2012) De novo assembly of the carrot mitochondrial genome using next generation sequencing of whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome. BMC Plant Biol 12:61. doi:10.1186/1471-2229-12-61
Jansen RK, Kaittanis C, Saski C et al (2006) Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences: effects of taxon sampling and phylogenetic methods on resolving relationships among rosids. BMC Evol Biol 6:32. doi:10.1186/1471-2148-6-32
Janska H, Sarria R, Woloszynska M et al (1998) Stoichiometric shifts in the common bean mitochondrial genome leading to male sterility and spontaneous reversion to fertility. Plant Cell 10:1163–1180
Joyce PBM, Gray MW (1988) Nucleotide sequence of a wheat mitochondrial glutamine tRNA gene. Nucleic Acids Res 16:1210
Kahlau S, Bock R (2008) Plastid transcriptomics and translatomics of tomato fruit development and chloroplast-to-chromoplast differentiation: chromoplast gene expression largely serves the production of a single protein. Plant Cell 20:856–874. doi:10.1105/tpc.107.055202
Kahlau S, Aspinall S, Gray JC, Bock R (2006) Sequence of the tomato chloroplast DNA and evolutionary comparison of solanaceous plastid genomes. J Mol Evol 63:194–207. doi:10.1007/s00239-005-0254-5
Kajander OA, Rovio AT, Majamaa K et al (2000) Human mtDNA sublimons resemble rearranged mitochondrial genomes found in pathological states. Hum Mol Genet 9:2821–2835. doi:10.1093/hmg/9.19.2821
Kanazawa A, Hirai A (1994) Reversible changes in the composition of the population of mtdnas during dedifferentiation and regeneration in tobacco. Genetics 138:865–870
Kanevski I, Maliga P (1994) Relocation of the plastid rbcL gene to the nucleus yields functional ribulose-1,5-bisphosphate carboxylase in tobacco chloroplasts. Proc Natl Acad Sci USA 91:1969–1973
Kato T, Kaneko T, Sato S et al (2000) Complete structure of the chloroplast genome of a legume, Lotus japonicus. DNA Res 7:323–330
Keeling PJ (2010) The endosymbiotic origin, diversification and fate of plastids. Philos Trans R Soc Lond B Biol Sci 365:729–748. doi:10.1098/rstb.2009.0103
Kim K-J, Lee H-L (2004) Complete chloroplast genome sequences from Korean ginseng (Panax schinseng Nees) and comparative analysis of sequence evolution among 17 vascular plants. DNA Res 11:247–261
Kim J-S, Jung JD, Lee J-A et al (2006) Complete sequence and organization of the cucumber (Cucumis sativus L. cv. Baekmibaekdadagi) chloroplast genome. Plant Cell Rep 25:334–340. doi:10.1007/s00299-005-0097-y
Kleine T, Maier UG, Leister D (2009) DNA transfer from organelles to the nucleus: the idiosyncratic genetics of endosymbiosis. Annu Rev Plant Biol 60:115–138. doi:10.1146/annurev.arplant.043008.092119
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. doi:10.1007/s00294-006-0082-1
Kode V, Mudd EA, Iamtham S, Day A (2005) The tobacco plastid accD gene is essential and is required for leaf development. Plant J Cell Mol Biol 44:237–244. doi:10.1111/j.1365-313X.2005.02533.x
Kubo T, Nishizawa S, Sugawara A et al (2000) The complete nucleotide sequence of the mitochondrial genome of sugar beet (Beta vulgaris L.) reveals a novel gene for tRNA(Cys)(GCA). Nucleic acids research 28:2571–2576
Kugita M (2003) The complete nucleotide sequence of the hornwort (Anthoceros formosae) chloroplast genome: insight into the earliest land plants. Nucleic Acids Res 31:716–721. doi:10.1093/nar/gkg155
Kurland CG, Andersson SG (2000) Origin and evolution of the mitochondrial proteome. Microbiol Mol Biol Rev MMBR 64:786–820
Kuroda H, Maliga P (2003) The plastid clpP1 protease gene is essential for plant development. Nature 425:86–89. doi:10.1038/nature01909
Kuzmin EV, Duvick DN, Newton KJ (2005) A mitochondrial mutator system in maize. Plant Physiol 137:779–789. doi:10.1104/pp.104.053611.1
Leaver CJ, Gray MW (1982) Mitochondrial genome organization and expression in higher plants. Annu Rev Plant Physiol 33:373–402. doi:10.1146/annurev.pp.33.060182.002105
Lee S-B, Kaittanis C, Jansen RK et al (2006) The complete chloroplast genome sequence of Gossypium hirsutum: organization and phylogenetic relationships to other angiosperms. BMC Genom 7:61. doi:10.1186/1471-2164-7-61
Lee H-L, Jansen RK, Chumley TW, Kim K-J (2007) Gene relocations within chloroplast genomes of Jasminum and Menodora (Oleaceae) are due to multiple, overlapping inversions. Mol Biol Evol 24:1161–1180. doi:10.1093/molbev/msm036
Legen J, Kemp S, Krause K et al (2002) Comparative analysis of plastid transcription profiles of entire plastid chromosomes from tobacco attributed to wild-type and PEP-deficient transcription machineries. Plant J Cell Mol Biol 31:171–188
Lemieux C, Otis C, Turmel M (2007) A clade uniting the green algae Mesostigma viride and Chlorokybus atmophyticus represents the deepest branch of the Streptophyta in chloroplast genome-based phylogenies. BMC Biol 5:2. doi:10.1186/1741-7007-5-2
Lerbs-Mache S (2000) Regulation of rDNA transcription in plastids of higher plants. Biochimie 82:525–535
Li L, Wang B, Liu Y, Qiu Y-L (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. doi:10.1007/s00239-009-9240-7
Lopez JV, Yuhki N, Masuda R et al (1994) Numt, a recent transfer and tandem amplification of mitochondrial DNA to the nuclear genome of the domestic cat. J Mol Evol 39:174–190
Ma P-F, Guo Z-H, Li D-Z (2012) Rapid sequencing of the bamboo mitochondrial genome using Illumina technology and parallel episodic evolution of organelle genomes in grasses. PLoS One 7:e30297
Mackenzie S, McIntosh L (1999) Higher plant mitochondria. Plant Cell 11:571–586
Margulis L, Bermudes D (1985) Symbiosis as a mechanism of evolution: status of cell symbiosis theory. Symbiosis (Philadelphia, PA) 1:101–124
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
Martin W, Stoebe B, Goremykin V et al (1998) Gene transfer to the nucleus and the evolution of chloroplasts. Nature 393:162–165. doi:10.1038/30234
Martínez-Zapater JM, Gil P, Capel J, Somerville CR (1992) Mutations at the Arabidopsis CHM locus promote rearrangements of the mitochondrial genome. Plant Cell 4:889–899. doi:10.1105/tpc.4.8.889
Maul JE, Lilly JW, Cui L et al (2002) The Chlamydomonas reinhardtii plastid chromosome: islands of genes in a sea of repeats. Plant Cell 14:2659–2679. doi:10.1105/tpc.006155.present
Mereschkowski C (1905) Über Natur und Ursprung der Chromatophoren im Pflanzenreiche. Biol Centralbl 25:593–604
Moore MJ, Dhingra A, Soltis PS et al (2006) Rapid and accurate pyrosequencing of angiosperm plastid genomes. BMC Plant Biol 6:17. doi:10.1186/1471-2229-6-17
Nägeli C (1846) Über Polysiphonia und Herposiphonia. Zeitschrift für wissenschaftliche Botanik 4:207–256
Nass S, Nass MM (1963) Intramitochondrial fibers with DNA characteristics. II. Enzymatic and other hydrolytic treatments. J Cell Biol 19:613–629
Nedelcu AM, Lee RW, Lemieux C et al (2000) The complete mitochondrial DNA sequence of Scenedesmus obliquus reflects an intermediate stage in the evolution of the green algal mitochondrial genome. Genome Res 10:819–831
Nei M, Kumar S (2000) Molecular evolution and phylogenetics. Oxford University Press, Oxford
Notsu Y, Masood S, Nishikawa T et al (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 MGG 268:434–445. doi:10.1007/s00438-002-0767-1
Oda K, Yamato K, Ohta E 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
Ogihara Y, Isono K, Kojima T et al (2002) Structural features of a wheat plastome as revealed by complete sequencing of chloroplast DNA. Mol Genet Genomics MGG 266:740–746. doi:10.1007/s00438-001-0606-9
Ogihara Y, Yamazaki Y, Murai K et al (2005) Structural dynamics of cereal mitochondrial genomes as revealed by complete nucleotide sequencing of the wheat mitochondrial genome. Nucleic Acids Res 33:6235–6250. doi:10.1093/nar/gki925
Ohyama K (1996) Chloroplast and mitochondrial genomes from a liverwort, Marchantia polymorpha: gene organization and molecular evolution. Biosci Biotechnol Biochem 60:16–24
Ohyama K, Fukuzawa H, Kohchi T et al (1986) Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA. Nature 322:572–574. doi:10.1038/322572a0
Oldenburg DJ, Bendich AJ (1996) Size and structure of replicating mitochondrial DNA in cultured tobacco cells. Plant Cell 8:447–461. doi:10.1105/tpc.8.3.447
Palmer JD (1991) CHAPTER 2—plastid chromosomes: structure and evolution. In: Molecular The (ed) Plastids IVBT-TMB of biology of plastids. Academic Press, London, pp 5–53
Palmer JD, Herbon LA (1987) Unicircular structure of the Brassica hirta mitochondrial genome. Curr Genet 11:565–570
Palmer JD, Zamir D (1982) Chloroplast DNA evolution and phylogenetic relationships in Lycopersicon. Proc Natl Acad Sci USA 79:5006–5010
Palmer JD, Adams KL, Cho Y et al (2000) Dynamic evolution of plant mitochondrial genomes: mobile genes and introns and highly variable mutation rates. Proc Natl Acad Sci USA 97:6960–6966
Pfannschmidt T, Nilsson A, Tullberg A et al (1999) Direct transcriptional control of the chloroplast genes psbA and psaAB adjusts photosynthesis to light energy distribution in plants. IUBMB Life 48:271–276. doi:10.1080/713803507
Phillips AL (1985) Restriction map and clone bank of tomato plastid DNA. Curr Genet 10:147–152
Pichersky E, Tanksley SD (1988) Chloroplast DNA sequences integrated into an intron of a tomato nuclear gene. Mol Gen Genet 215:65–68
Pichersky E, Logsdon JM, McGrath JM, Stasys RA (1991) Fragments of plastid DNA in the nuclear genome of tomato: prevalence, chromosomal location, and possible mechanism of integration. Mol Gen Genet 225:453–458
Piechulla B, Imlay KRC, Gruissem W (1985) Plastid gene expression during fruit ripening in tomato. Plant Mol Biol 5:373–384
Pombert J-F, 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. doi:10.1093/molbev/msh099
Pombert J-F, Lemieux C, Turmel M (2006) The complete chloroplast DNA sequence of the green alga Oltmannsiellopsis viridis reveals a distinctive quadripartite architecture in the chloroplast genome of early diverging ulvophytes. BMC Biol 4:3. doi:10.1186/1741-7007-4-3
Popescu CE, Lee RW (2007) Mitochondrial genome sequence evolution in Chlamydomonas. Genetics 175:819–826. doi:10.1534/genetics.106.063156
Raubeson LA, Peery R, Chumley TW et al (2007) Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus. BMC Genomics 8:174. doi:10.1186/1471-2164-8-174
Ris H, Plaut W (1962) Ultrastructure of DNA-containing areas in the chloroplast of Chlamydomonas. J Cell Biol 13:383–391
Rivarola M, Foster JT, Chan AP et al (2011) Castor bean organelle genome sequencing and worldwide genetic diversity analysis. PLoS One 6:e21743
Robbens S, Derelle E, Ferraz C et al (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. doi:10.1093/molbev/msm012
Rodríguez-Moreno L, González VM, Benjak A et al (2011) Determination of the melon chloroplast and mitochondrial genome sequences reveals that the largest reported mitochondrial genome in plants contains a significant amount of DNA having a nuclear origin. BMC Genom 12:424. doi:10.1186/1471-2164-12-424
Rogalski M, Schöttler MA, Thiele W et al (2008) Rpl33, a nonessential plastid-encoded ribosomal protein in tobacco, is required under cold stress conditions. Plant Cell 20:2221–2237. doi:10.1105/tpc.108.060392
Rosso SW (1968) The ultrastructure of chromoplast development in red tomatoes. J Ultrastruct Res 25:307–322
Ruhlman T, Lee S-B, Jansen RK et al (2006) Complete plastid genome sequence of Daucus carota: implications for biotechnology and phylogeny of angiosperms. BMC Genom 7:222. doi:10.1186/1471-2164-7-222
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Sakamoto W, Tan S-H, Murata M, Motoyoshi F (1997) An unusual mitochondrial atp9-rpl16 cotranscript found in the maternal distorted leaf mutant of Arabidopsis thaliana: implication of GUG as an initiation codon in plant mitochondria. Plant Cell Physiol 38:975–979
Saski C, Lee S-B, Daniell H et al (2005) Complete chloroplast genome sequence of Gycine max and comparative analyses with other legume genomes. Plant Mol Biol 59:309–322. doi:10.1007/s11103-005-8882-0
Saski C, Lee S-B, Fjellheim S et al (2007) Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera, and comparative analyses with other grass genomes. TAG Theor Appl Genet 115:571–590. doi:10.1007/s00122-007-0567-4
Sato S, Nakamura Y, Kaneko T et al (1999) Complete structure of the chloroplast genome of Arabidopsis thaliana. DNA Res 6:283–290
Schatz G, Haslbrunner E, Tuppy H (1964) Deoxyribonucleic acid associated with yeast mitochondria. Biochem Biophys Res Commun 15:127–132
Schmidt EW (1913) Pflanzliche Mitochondrien. Progressus rei botanicae 4:164–183
Schmitz-Linneweber C, Regel R, Du TG et al (2002) The plastid chromosome of Atropa belladonna and its comparison with that of Nicotiana tabacum: the role of RNA editing in generating divergence in the process of plant speciation. Mol Biol Evol 19:1602–1612
Schön A, Krupp G, Gough S et al (1986) The RNA required in the first step of chlorophyll biosynthesis is a chloroplast glutamate tRNA. Nature 322:281–284
Scott NS, Timmis JN (1984) Homologies between nuclear and plastid DNA in spinach. Theor Appl Genet 67:279–288
Sharma MR, Wilson DN, Datta PP et al (2007) Cryo-EM study of the spinach chloroplast ribosome reveals the structural and functional roles of plastid-specific ribosomal proteins. Proc Natl Acad Sci USA 104:19315–19320. doi:10.1073/pnas.0709856104
Shikanai T, Kaneko H, Nakata S et al (1998) Mitochondrial genome structure of a cytoplasmic hybrid between tomato and wild potato. Plant Cell Rep 17:832–836. doi:10.1007/s002990050493
Shikanai T, Shimizu K, Ueda K et al (2001) The chloroplast clpP gene, encoding a proteolytic subunit of ATP-dependent protease, is indispensable for chloroplast development in tobacco. Plant Cell Physiol 42:264–273
Shinozaki K, Ohme M, Tanaka M et al (1986) The complete nucleotide sequence of the tobacco chloroplast genome: its gene organization and expression. EMBO J 5:2043–2049
Smith DR, Lee RW (2008) Mitochondrial genome of the colorless green alga Polytomella capuana: a linear molecule with an unprecedented GC content. Mol Biol Evol 25:487–496. doi:10.1093/molbev/msm245
Steane DA (2005) Complete nucleotide sequence of the chloroplast genome from the Tasmanian bluegum, Eucalyptus globulus (Myrtaceae). DNA Res 12:215–220. doi:10.1093/dnares/dsi006
Stern DB, Palmer JD (1984) Extensive and widespread homologies between mitochondrial DNA and chloroplast DNA in plants. Proc Natl Acad Sci USA 81:1946–1950
Stutzt B, Noll H (1967) Polysomies in plants: evidence for three classes of ribosomal RNA in nature. Proc Natl Acad Sci USA 57:774–781
Sugiura M (1992) The chloroplast genome. In: Schilperoort R, Dure L (eds) 10 Years plant molecular biology. Springer, Netherlands, pp 149–168
Sugiyama Y, Watase Y, Nagase M et al (2004) Timing of tRNA gene transfer from chloroplast to mitochondrion revealed by genomic analysis of dicotyledonous plant mitochondria. Endocytobiosis Cell Res 15:77–86
Sugiyama Y, Watase Y, Nagase M et al (2005) The complete nucleotide sequence and multipartite organization of the tobacco mitochondrial genome: comparative analysis of mitochondrial genomes in higher plants—supp info. Mol Genet Genomics 272:303–315
Sun Q, Wang K, Yoshimura A, Doi K (2002) Genetic differentiation for nuclear, mitochondrial and chloroplast genomes in common wild rice (Oryza rufipogon Griff.) and cultivated rice (Oryza sativa L.). TAG Theor Appl Genet 104:1335–1345. doi:10.1007/s00122-002-0878-4
Tamura K, Peterson D, Peterson N et al (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739. doi:10.1093/molbev/msr121
Tanaka K, Oikawa K, Ohta N et al (1996) Nuclear encoding of a chloroplast RNA polymerase sigma subunit in a red alga. Science (New York, NY) 272:1932–1935
Taylor DR, Olson MS, McCauley DE (2001) A quantitative genetic analysis of nuclear-cytoplasmic male sterility in structured populations of Silene vulgaris. Genetics 158:833–841
Terasawa K, Odahara M, Kabeya Y et al (2007) The mitochondrial genome of the moss Physcomitrella patens sheds new light on mitochondrial evolution in land plants. Mol Biol Evol 24:699–709. doi:10.1093/molbev/msl198
The Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–641. doi:10.1038/nature11119
Thorsness PE, Weber ER (1996) Escape and migration of nucleic acids between chloroplasts, mitochondria, and the nucleus. Int Rev Cytol 165:207–234
Tian X, Zheng J, Hu S (2006) The rice mitochondrial genomes and their variations. Plant Physiol 140:401–410. doi:10.1104/pp.105.070060.Palmer
Tiller N, Weingartner M, Thiele W et al (2012) The plastid-specific ribosomal proteins of Arabidopsis thaliana can be divided into non-essential proteins and genuine ribosomal proteins. Plant J Cell Mol Biol 69:302–316. doi:10.1111/j.1365-313X.2011.04791.x
Timmis JN, Scot SN (1983) Sequence homology between spinach nuclear and chloroplast genomes. Nature 305:65–67
Timmis JN, Ayliffe MA, Huang CY, Martin W (2004) Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat Rev Genet 5:123–135. doi:10.1038/nrg1271
Tullberg A, Alexciev K, Pfannschmidt T, Allen JF (2000) Photosynthetic electron flow regulates transcription of the psaB gene in pea (Pisum sativum L.) chloroplasts through the redox state of the plastoquinone pool. Plant Cell Physiol 41:1045–1054. doi:10.1093/pcp/pcd031
Turmel M, Lemieux C, Burger G et al (1999a) The complete mitochondrial DNA sequences of Nephroselmis olivacea and Pedinomonas minor. Two radically different evolutionary patterns within green algae. Plant Cell 11:1717–1730
Turmel M, Otis C, Lemieux C (1999b) The complete chloroplast DNA sequence of the green alga Nephroselmis olivacea: insights into the architecture of ancestral chloroplast genomes. Proc Natl Acad Sci USA 96:10248–10253
Turmel M, Otis C, Lemieux C (2002a) 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
Turmel M, Otis C, Lemieux C (2002b) 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. doi:10.1073/pnas.162203299
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. doi:10.1105/tpc.013169.these
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
Wakasugi T, Tsudzuki J, Ito S et al (1994) Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii. Proc Natl Acad Sci USA 91:9794–9798
Wakasugi T, Nagai T, Kapoor M et al (1997) Complete nucleotide sequence of the chloroplast genome from the green alga Chlorella vulgaris: the existence of genes possibly involved in chloroplast division. Proc Natl Acad Sci USA 94:5967–5972
Wallin IE (1923) The University of Chicago. Am Nat 57:255–261
Wang B, Xue J, Li L et al (2009) The complete mitochondrial genome sequence of the liverwort Pleurozia purpurea reveals extremely conservative mitochondrial genome evolution in liverworts. Curr Genet 55:601–609. doi:10.1007/s00294-009-0273-7
Wang D, Rousseau-Gueutin M, Timmis JN (2012) Plastid sequences contribute to some plant mitochondrial genes. Mol Biol Evol 29:1707–1711. doi:10.1093/molbev/mss016
Ward BL, Anderson RS, Bendich AJ (1981) The mitochondrial genome is large and variable in a family of plants (Cucurbitaceae). Cell 25:793–803
Wolf PG, Rowe CA, Sinclair RB, Hasebe M (2003) Complete nucleotide sequence of the chloroplast genome from a leptosporangiate fern, Adiantum capillus-veneris L. DNA Res 10:59–65
Woloszynska M, Kieleczawa J, Ornatowska M et al (2001) The origin and maintenance of the small repeat in the bean mitochondrial genome. Mol Genet Genomics 265:865–872. doi:10.1007/s004380100481
Xue J-Y, Liu Y, Li L et al (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. doi:10.1007/s00294-009-0279-1
Yamato KT, Newton KJ (1999) Heteroplasmy and homoplasmy for maize mitochondrial mutants: a rare homoplasmic nad4 deletion mutant plant. J Hered 90:369–373. doi:10.1093/jhered/90.3.369
Yu Q, Tong E, Skelton RL et al (2009) A physical map of the papaya genome with integrated genetic map and genome sequence. BMC Genom 10:371. doi:10.1186/1471-2164-10-371
Yukawa M, Tsudzuki T, Sugiura M (2006) The chloroplast genome of Nicotiana sylvestris and Nicotiana tomentosiformis: complete sequencing confirms that the Nicotiana sylvestris progenitor is the maternal genome donor of Nicotiana tabacum. Mol Genet Genomics MGG 275:367–373. doi:10.1007/s00438-005-0092-6
Zheng L-Y, Guo X-S, He B et al (2011) Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor). Genome Biol 12:R114. doi:10.1186/gb-2011-12-11-r114
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Lichtenstein, G., Conte, M., Asis, R., Carrari, F. (2016). Chloroplast and Mitochondrial Genomes of Tomato. In: Causse, M., Giovannoni, J., Bouzayen, M., Zouine, M. (eds) The Tomato Genome. Compendium of Plant Genomes. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-53389-5_7
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