Skip to main content
SpringerLink
Log in

Plastid Genomes of Seed Plants

  • Chapter
  • First Online:
Genomics of Chloroplasts and Mitochondria

Part of the book series: Advances in Photosynthesis and Respiration ((AIPH,volume 35))

Summary

The field of comparative plastid genomics has burgeoned during the past decade, largely due to the availability of rapid, less expensive genome sequencing technologies. Currently there are 200 plastid genomes (plastomes) publicly available with 65% of these from seed plants. Comparative analyses have demonstrated that there is an overall stability in plastome architecture, gene and intron content, and gene order across seed plants. However, a number of unrelated lineages of both gymnosperms and angiosperms do not follow this pattern and have experienced considerable genomic upheaval. Within angiosperms these lineages with highly rearranged plastomes exhibit three other phenomena: highly accelerated rates of nucleotide substitutions, an increase in the number of dispersed repeats, many of which are associated with rearrangement endpoints, and biparental plastid inheritance. The correlation between genomic upheaval and these other phenomena suggest that aberrant DNA repair mechanisms may be involved in destabilizing these plastid genomes. Experimental studies support this idea because knocking out DNA repair genes destabilizes plastomes. Further studies of nuclear-plastid interactions, especially in seed plant lineages with highly rearranged plastomes, are needed to clarify the causes of the plastome instability. The large number of plastome sequences has also provided valuable data for resolving phylogenetic relationships among seed plants. This is especially true for angiosperms where these data have been instrumental in clarifying relationships among the early diverging clades, an endeavor that had stymied plant biologists for over a decade. The most recent plastome phylogenies clearly identify Amborella as the earliest diverging lineage of flowering plants and provide strong support for the position of magnoliids as sister to a large clade that includes eudicots and monocots. This robust phylogenetic estimate provides an evolutionary framework for examining patterns and rates of change in plastid genomes across angiosperms.

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
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

Institutional subscriptions

Abbreviations

bp –:

Basepair;

indel –:

Insertion/deletion;

IR –:

Inverted repeat;

IRLC –:

Inverted repeat lacking clade;

kb –:

Kilobase;

LSC –:

Large single copy region;

PEP –:

Plastid encoded polymerase;

SSC –:

Small single copy region

References

  • Angiosperm Phylogeny Group [APG] (2009) An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Bot J Linn Soc 161:105–121

    Google Scholar 

  • Atherton RA, McComish BJ, Shepherd LD, Berry LA, Albert NW, Lockhart PJ (2010) Whole genome sequencing of enriched chloroplast DNA using the Illumina GAII platform. BMC Plant Methods 6:22

    Google Scholar 

  • Belda E, Moya A, Silva FJ (2005) Genome rearrangement distances and gene order phylogeny in gamma-Proteobacteria. Mol Biol Evol 22:1456–1467

    PubMed  CAS  Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Bennett JR, Mathews S (2006) Phylogeny of the parasitic plant family Orobanchaceae inferred from phytochrome A. Am J Bot 93:1039–1051

    PubMed  CAS  Google Scholar 

  • Birky CWJR (1995) Uniparental inheritance of mitochondrial and chloroplast genes: mechanisms and evolution. Proc Natl Acad Sci USA 92:11331–11338

    PubMed  CAS  Google Scholar 

  • Blazier JC, Guisinger MM, Jansen RK (2011) Recent loss of plastid-encoded ndh genes within Erodium (Geraniaceae). Plant Mol Biol 76:263–272

    Google Scholar 

  • Bock R (2007) Structure, function, and inheritance of plastid genomes. In: Bock R (ed) Cell and molecular biology of plastids. Springer, Berlin/Heidelberg, pp 1610–2096

    Google Scholar 

  • Boudreau E, Turmel M (1995) Gene rearrangements in Chlamydomonas chloroplast DNAs are accounted for by inversions and by expansion/contraction of the inverted repeat. Plant Mol Biol 27:351–364

    PubMed  CAS  Google Scholar 

  • Bourque G, Pevzner P (2002) Genome-scale evolution: reconstructing gene orders in the ancestral species. Genome Res 12:26–36

    PubMed  CAS  Google Scholar 

  • Braukmann TW, Kuzmina M, Stefanovic S (2009) Loss of all plastid ndh genes in Gnetales and conifers: extent and evolutionary significance for the seed plant phylogeny. Curr Genet 55:323–337

    PubMed  CAS  Google Scholar 

  • Bruneau A, Doyle JJ, Palmer JD (1990) A chloroplast DNA inversion as a subtribal character in the Phaseoleae (Leguminosae). Syst Bot 15:378–386

    Google Scholar 

  • Bubunenko MG, Schmidt J, Subramanian AR (1994) Protein substitution in chloroplast ribosome evolution. A eukaryotic cytosolic protein has replaced its organelle homologue (L23) in spinach. J Mol Biol 240:28–41

    PubMed  CAS  Google Scholar 

  • Burleigh JG, Mathews S (2004) Phylogenetic signal in nucleotide data from seed plants: implications for resolving the seed plant tree of life. Am J Bot 91:1599–1613

    PubMed  CAS  Google Scholar 

  • Cai Z, Penaflor C, Kuehl JV, Leebens-Mack J, Carlson J, dePamphilis CW, Jansen RK (2006) Complete plastid genome sequences of Drimys, Liriodendron, and Piper: implications for the phylogeny of magnoliids. BMC Evol Biol 6:77

    PubMed  Google Scholar 

  • Cai Z, Guisinger M, Kim HG, Ruck E, Blazier JC, McMurtry V, Kuehl JV, Boore J, Jansen RK (2008) Extensive reorganization of the plastid genome of Trifolium subterraneum (Fabaceae) is associated with numerous repeated sequences and novel DNA insertions. J Mol Evol 67:696–704

    PubMed  CAS  Google Scholar 

  • Chang C-C, Lin H-C, Lin I-P, Chow T-Y, Chen H-H, Chen W-H, Cheng C-H, Lin C-Y, Liu S-M, Chang C-C, Chaw S-M (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

    PubMed  CAS  Google Scholar 

  • Chaw S-M, Chang C-C, Chen H-L, Li W-H (2004) Dating the monocot dicot divergence and the origin of core eudicots using whole chloroplast genomes. J Mol Evol 58:424–441

    PubMed  CAS  Google Scholar 

  • Chiu WL, Sears BB (1993) Plastome-genome interactions affect plastid transmission in Oenothera. Genetics 133:989–997

    PubMed  CAS  Google Scholar 

  • Chumley TW, Palmer JD, Mower JP, Fourcade HM, Calie PJ, Boore JL, Jansen RK (2006) The complete chloroplast genome sequence of Pelargonium x hortorum: organization and evolution of the largest and most highly rearranged chloroplast genome of land plants. Mol Biol Evol 23:2175–2190

    PubMed  CAS  Google Scholar 

  • Chung H-J, Jung JD, Park H-W, Kim J-H, Cha HW, Min SR, Jeong W-J, Liu JR (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

    PubMed  CAS  Google Scholar 

  • Clegg MT, Brown ADH, Whitfield PR (1984) Chloroplast DNA diversity in wild and cultivated barley: implications for genetic conservation. Genet Res 43:339–343

    CAS  Google Scholar 

  • Conant GC, Wolfe KH (2008) GenomeVx: simple web-based creation of editable circular chromosome maps. Bioinformatics 24:861–862

    PubMed  CAS  Google Scholar 

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

    Google Scholar 

  • Cosner ME (1993) Phylogenetic and molecular evolutionary studies of chloroplast DNA variation in the Campanulaceae. PhD thesis, The Ohio State University, Columbus

    Google Scholar 

  • Cosner ME, Jansen RK, Palmer JD, Downie SR (1997) The highly rearranged chloroplast genome of Trachelium caeruleum (Campanulaceae): multiple inversions, inverted repeat expansion and contraction, transposition, insertions/deletions, and several repeat families. Curr Genet 31:419–429

    PubMed  CAS  Google Scholar 

  • Cosner ME, Raubeson LA, Jansen RK (2004) Chloroplast DNA rearrangements in Campanulaceae: phylogenetic utility of highly rearranged genomes. BMC Evol Biol 4:27

    PubMed  Google Scholar 

  • Cronn R, Liston A, Parks M, Gernandt D, Shen R, Mockler T (2008) Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by synthesis technology. Nucleic Acids Res 36:e122

    PubMed  Google Scholar 

  • Cruzan MB, Arnold ML, Carney SE, Wollenberg KR (1993) CpDNA inheritance in interspecific crosses and evolutionary inference in Louisiana irises. Am J Bot 80:344–350

    CAS  Google Scholar 

  • Cusack BP, Wolfe KH (2007) When gene marriages don’t work: divorce by subfunctionalization. Trends Genet 23:270–272

    PubMed  CAS  Google Scholar 

  • Daniell H, Lee S-B, Grevich J, Saski C, Guda C, Tompkins J, Jansen RK (2006) Complete chloroplast genome sequences of Solanum tuberosum, Solanum lycopersicum and comparative analyses with other Solanaceae genomes. Theor Appl Genet 112:1503–1518

    PubMed  CAS  Google Scholar 

  • Daniell H, Wurdack KJ, Kanagaraj A, Lee S-B, Saski C, Jansen RK (2008) The complete nucleotide sequence of the cassava (Manihot esculenta) chloroplast genome and multiple losses of the atpF intron in Malpighiales. Theor Appl Genet 116:723–737

    PubMed  CAS  Google Scholar 

  • Darling AE, Mau B, Perna NT (2010) Progressive mauve: multiple genome alignment with gene gain, loss, and rearrangement. PLoS One 5:e11147

    PubMed  Google Scholar 

  • Decker-Walters DS, Chung SM, Staub JE (2004) Plastid sequence evolution: a new pattern of nucleotide substitutions in the Cucurbitaceae. J Mol Evol 58:606–614

    PubMed  CAS  Google Scholar 

  • Delannoy E, Fujii S, des Frances CC, Brundrett M, Small I (2011) Rampant gene loss in the underground orchid Rhizanthella gardneri highlights evolutionary constraints on plastid genomes. Mol Biol Evol 28:2077–2086

    Google Scholar 

  • dePamphilis CW, Young ND, Wolfe AD (1997) Evolution of plastid gene rps2 in a lineage of hemiparasitic and holoparasitic plants: many losses of photosynthesis and complex patterns of rate variation. Proc Natl Acad Sci USA 94:7367–7372

    PubMed  CAS  Google Scholar 

  • Downie SR, Palmer JD (1992) Use of chloroplast DNA rearrangements in reconstructing plant phylogeny. In: Soltis PS, Soltis DE, Doyle JJ (eds) Molecular systematics of plants. Chapman and Hall, New York, pp 14–35

    Google Scholar 

  • Downie SR, Llanas E, Katz-Downie DS (1996) Multiple independent losses of the rpoC1 intron in angiosperm chloroplast DNAs. Syst Bot 21:135–151

    Google Scholar 

  • Doyle JA, Donoghue MJ (1986) Seed plant phylogeny and the origin of angiosperms: an experimental cladistic approach. Bot Rev 52:321–431

    Google Scholar 

  • Doyle JJ, Doyle JL, Palmer JD (1995) Multiple independent losses of two genes and one intron from legume chloroplast genomes. Syst Bot 20:272–294

    Google Scholar 

  • Doyle JJ, Doyle JL, Palmer JD (1996) The distribution and phylogenetic significance of a 50-kb chloroplast DNA inversion in the flowering plant family Leguminosae. Mol Phylogenet Evol 5:429–438

    PubMed  CAS  Google Scholar 

  • Drummond AJ, Ashton B, Buxton S, Cheung M, Cooper A, Heled J, Kearse M, Moir R, Stones-Havas S, Sturrock S, Thierer T, Wilson A (2010) Geneious v5.1. http://www.geneious.com

  • Fan WH, Woelfle MA, Mosig G (1995) Two copies of a DNA element, ‘Wendy’, in the chloroplast chromosome of Chlamydomonas reinhardtii between rearranged gene clusters. Plant Mol Biol 29:63–80

    PubMed  CAS  Google Scholar 

  • Funk HT, Berg S, Krupinska K, Maier UG, Krause K (2007) Complete DNA sequences of the plastid genomes of two parasitic flowering plant species, Cuscuta reflexa and Cuscuta gronovii. BMC Plant Biol 7:45

    PubMed  Google Scholar 

  • Gantt JS, Baldauf SL, Calie PJ, Weeden NF, Palmer JD (1991) Transfer of rpl22 to the nucleus greatly preceded its loss from the chloroplast and involved the gain of an intron. EMBO J 10:3073–3078

    PubMed  CAS  Google Scholar 

  • Gao L, Su Y-J, Wang T (2010) Plastid genome sequencing, comparative genomics, and phylogenomics: current status and prospects. J Syst Evol 48:77–93

    Google Scholar 

  • Gaut BS (1998) Molecular clocks and nucleotide substitution rates in higher plants. In: Hecht MK (ed) Evolutionary biology. Plenum Press, New York, pp 93–120

    Google Scholar 

  • Gaut BS, Muse SV, Clegg MT (1993) Relative rates of nucleotide substitution in the chloroplast genome. Mol Phylogenet Evol 2:89–96

    PubMed  CAS  Google Scholar 

  • Golenberg EM, Clegg MT, Durbin ML, Doebley J, Ma DP (1993) Evolution of a noncoding region of the chloroplast genome. Mol Phylogenet Evol 2:52–64

    PubMed  CAS  Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • Goremykin VV, Hirsch-Ernst KI, Wolfl S, Hellwig FH (2004) The chloroplast genome of Nymphaea alba: whole-genome analyses and the problem of identifying the most basal angiosperm. Mol Biol Evol 21:1445–1454

    PubMed  CAS  Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • Gornicki P, Faris J, King I, Podkowinski J, Gill B, Haselkorn R (1997) Plastid localized acetyl-Co-A carboxylase of bread wheat is encoded by a single gene on each of the three ancestral chromosome sets. Proc Natl Acad Sci USA 94:14179–14184

    PubMed  CAS  Google Scholar 

  • Goulding SE, Olmstead RG, Morden CW, Wolfe KH (1996) Ebb and flow of the chloroplast inverted repeat. Mol Gen Genet 252:195–206

    PubMed  CAS  Google Scholar 

  • Gray BN, Ahner BA, Hanson MR (2009) Extensive homologous recombination between introduced and native regulatory plastid DNA elements in transplastomic plants. Transgenic Res 18:559–572

    PubMed  CAS  Google Scholar 

  • Guisinger MM, Kuehl JV, Boore JL, Jansen RK (2008) Genome-wide analyses of Geraniaceae plastid DNA reveal unprecedented patterns of increased nucleotide substitutions. Proc Natl Acad Sci USA 105:18424–18429

    PubMed  CAS  Google Scholar 

  • Guisinger MM, Chumley TW, Kuehl JV, Boore JL, Jansen RK (2010) Implications of the plastid genome sequence of Typha (Typhaceae, Poales) for understanding genome evolution in Poaceae. J Mol Evol 70:149–166

    PubMed  CAS  Google Scholar 

  • Guisinger MM, Kuehl JV, Boore JL, Jansen RK (2011) Extreme reconfiguration of plastid genomes in the angiosperm family Geraniaceae: rearrangements, repeats, and codon usage. Mol Biol Evol 28:583–600

    PubMed  CAS  Google Scholar 

  • Haberle RC (2006) Phylogeny and comparative chloroplast genomics of the Campanulaceae. PhD thesis, University of Texas, Austin

    Google Scholar 

  • Haberle RC, Fourcade HM, Boore JL, Jansen RK (2008) Extensive rearrangements in the chloroplast genome of Trachelium caeruleum are associated with repeats and tRNA genes. J Mol Evol 66:350–361

    PubMed  CAS  Google Scholar 

  • Hagemann R (2004) The sexual inheritance of plant organelles. In: Daniell H, Chase C (eds) Molecular biology and biotechnology of plant organelles. Springer, Heidelberg, pp 93–113

    Google Scholar 

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

    PubMed  CAS  Google Scholar 

  • Hansen DR, Dastidar SG, Cai Z, Penaflor C, Kuehl V, Boore JL, Jansen RK (2007b) Phylogenetic and evolutionary implications of complete chloroplast genome sequences of four early diverging angiosperms: Buxus (Buxaceae), Chloranthus (Chloranthaceae), Dioscorea (Dioscoreaceae), and Illicium (Schisandraceae). Mol Phylogenet Evol 45:547–563

    PubMed  CAS  Google Scholar 

  • Hildebrand M, Hallick RB, Passavant CW, Bourque DP (1988) Trans-splicing in chloroplasts: the rps12 loci of Nicotiana tabacum. Proc Natl Acad Sci USA 85:372–376

    PubMed  CAS  Google Scholar 

  • Hirao T, Watanabe A, Kurita M, Kondo T, Takata K (2008) Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genome structure of coniferous species. BMC Plant Biol 8:70

    PubMed  Google Scholar 

  • Hiratsuka J, Shimada H, Whittier R, Ishibashi T, Sakamoto M, Mori M, Kondo C, Honji Y, Sun CR, Meng BY, Li YQ, Kanno A, Nishizawa Y, Hirai A, Shinozaki K, Sugiura M (1989) The complete sequence of the rice Oryza sativa chloroplast genome – intermolecular recombination between distinct transfer-RNA genes accounts for a major plastid DNA inversion during the evolution of the cereals. Mol Gen Genet 217:185–194

    PubMed  CAS  Google Scholar 

  • Hu YC, Zhang Q, Rao GY, Sodmergen (2008) Occurrence of plastids in the sperm cells of Caprifoliaceae: biparental plastid inheritance in angiosperms is unilaterally derived from maternal inheritance. Plant Cell Physiol 49:958–968

    PubMed  CAS  Google Scholar 

  • Ingvarsson PK, Ribstein S, Taylor DR (2003) Molecular evolution of insertions and deletions in the chloroplast genome of silene. Mol Biol Evol 20:1737–1740

    PubMed  CAS  Google Scholar 

  • Jansen RK, Palmer JD (1987) A chloroplast DNA inversion marks an ancient evolutionary split in the sunflower family (Asteraceae). Proc Natl Acad Sci USA 84:5818–5822

    PubMed  CAS  Google Scholar 

  • Jansen RK, Cai Z, Raubeson LA, Daniell H, de Pamphilis CW, Leebens-Mack J, Müller KF, Guisinger-Bellian M, Haberle RC, Hansen AK, Chumley TW, Lee SB, Peery R, McNeal JR, Kuehl JV, Boore JL (2007) Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns. Proc Natl Acad Sci USA 104:19369–19374

    PubMed  CAS  Google Scholar 

  • Jansen RK, Wojciechowski MF, Sanniyasi E, Lee S-B, Daniell H (2008) Complete plastid genome sequence of the chickpea (Cicer arietinum) and the phylogenetic distribution of rps12 and clpP intron losses among legumes (Fabaceae). Mol Phylogenet Evol 48:1204–1207

    PubMed  CAS  Google Scholar 

  • Jansen RK, Saski C, Lee S-B, Hansen AK, Daniell H (2011) Complete plastid genome sequences of three rosids (Castanea, Prunus, Theobroma): evidence for at least two independent transfers of rpl22 to the nucleus. Mol Biol Evol 28:835–847

    PubMed  CAS  Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • Kanno A, Watanabe K, Nakamura I, Hirai A (1993) Variations in chloroplast DNA from rice (Oryza sativa): differences between deletions mediated by short direct-repeat sequences within a single species. Theor Appl Genet 86:579–584

    CAS  Google Scholar 

  • Kawata M, Harada T, Shimamoto Y, Oono K, Takaiwa F (1997) Short inverted repeats function as hotspots of intermolecular recombination giving rise to oligomers of deleted plastid DNAs (ptDNAs). Curr Genet 31:179–184

    PubMed  CAS  Google Scholar 

  • Khan A, Khan IA, Asif H, Azim MK (2010) Current trends in chloroplast genome research. Afr J Biotechnol 9:3494–3500

    CAS  Google Scholar 

  • Kim K-J, Lee H-L (2004) Complete chloroplast genome sequence from Korean Ginseng (Panax schiseng Nees) and comparative analysis of sequence evolution among 17 vascular plants. DNA Res 11:247–261

    PubMed  CAS  Google Scholar 

  • Kim Y-K, Park C-W, Kim K-J (2009) Complete chloroplast DNA sequence from a Korean endemic genus, Megaleranthus saniculifolia, and its evolutionary implications. Mol Cells 27:365–381

    PubMed  CAS  Google Scholar 

  • Knox EB, Palmer JD (1999) The chloroplast genome arrangement of Lobelia thuliana (Lobeliaceae): expansion of the inverted repeat in an ancestor of the Campanulales. Plant Syst Evol 214:49–64

    Google Scholar 

  • Kolodner R, Tewari KK (1979) Inverted repeats in chloroplast DNA of higher plants. Proc Natl Acad Sci USA 76:41–45

    PubMed  CAS  Google Scholar 

  • Konishi T, Shinohara K, Yamada K, Sasaki Y (1996) Acetyl-CoA carboxylase in higher plants: most plants other than gramineae have both prokaryotic and eukaryotic forms of this enzyme. Plant Cell Physiol 37:117–122

    PubMed  CAS  Google Scholar 

  • Kuroiwa T (2010) Review of cytological studies on ­cellular and molecular mechanisms of uniparental (maternal or paternal) inheritance of plastid and mitochondrial genomes induced by active digestion of organelle nuclei (nucleoids). J Plant Res 123:207–230

    PubMed  CAS  Google Scholar 

  • Lavin M, Doyle JJ, Palmer JD (1990) Evolutionary significance of the loss of the chloroplast-DNA inverted repeat in the Leguminosae subfamily Papilionoideae. Evolution 44:390–402

    CAS  Google Scholar 

  • Lee DJ, Blake TK, Smith SE (1988) Biparental inheritance of chloroplast DNA and the existence of heteroplasmic cells in alfalfa. Theor Appl Genet 76:545–549

    CAS  Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • Leebens-Mack J, Raubeson LA, Cui L, Kuehl JV, Fourcade MH, Chumley TW, Boore JL, Jansen RK, dePamphilis CW (2005) Identifying the basal angiosperm node in chloroplast genome phylogenies: sampling one’s way out of the Felsenstein zone. Mol Biol Evol 22:1948–1963

    PubMed  CAS  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

    PubMed  CAS  Google Scholar 

  • Lin C-P, Huang J-P, Wu C-S, Hsu C-Y, Chaw S-M (2010) Comparative chloroplast genomics reveals the evolution of Pinaceae genera and subfamilies. Genome Biol Evol 2:504–517

    PubMed  Google Scholar 

  • Liu Q, Xue Q (2005) Comparative studies on codon usage pattern of chloroplasts and their host nuclear genes in four plant species. J Genet 84:55–62

    PubMed  CAS  Google Scholar 

  • Magee AM, Aspinall S, Rice DW, Cusack BP, Semon M, Perry AS, Stefanovic S, Milbourne D, Barth S, Palmer JD, Gray JC, Kavahagh TA, Wolfe KH (2010) Localized hypermutation and associated gene losses in legume chloroplast genomes. Genome Res 20:1700–1710

    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 A, Parent J, Véronneau-Lafortune F, Joyeux A, Lang BF, Brisson N (2009) Whirly proteins maintain plastid genome stability in Arabidopsis. Proc Natl Acad Sci USA 106:14693–14698

    PubMed  Google Scholar 

  • Masood MS, Nishikawa T, Fukuoka S, Njenga PK, Tsudzuki T, Kadowaki K (2004) The complete nucleotide sequence of wild rice (Oryza nivara) chloroplast genome: first genome wide comparative sequence analysis of wild and cultivated rice. Gene 340:133–139

    Google Scholar 

  • Mathews S (2009) Phylogenetic relationships among seed plants: persistent questions and the limits of molecular data. Am J Bot 96:228–236

    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

    PubMed  CAS  Google Scholar 

  • McCoy SR, Kuehl JV, Boore JL, Raubeson LA (2008) The complete plastid genome sequence of Welwitschia mirabilis: an unusually compact plastome with accelerated divergence rates. BMC Evol Biol 8:130

    PubMed  Google Scholar 

  • McNeal JR, Arumugunathan K, Kuehl JV, Boore JL, de Pamphilis CW (2007a) Systematics and plastid genome evolution of the cryptically photosynthetic parasitic plant genus Cuscuta (Convolvulaceae). BMC Biol 5:55

    PubMed  Google Scholar 

  • McNeal JR, Kuehl JV, Boore JL, dePamphilis CW (2007b) Complete plastid genome sequences suggest strong selection for retention of photosynthetic genes in the parasitic plant genus Cuscuta. BMC Plant Biol 7:57

    PubMed  Google Scholar 

  • Medgyesy P, Fejes E, Maliga P (1985) Interspecific chloroplast recombination in a Nicotiana somatic hybrid. Proc Natl Acad Sci USA 82:6960–6964

    PubMed  CAS  Google Scholar 

  • Metzlaff M, Pohlheim F, Börner T, Hagemann R (1982) Hybrid variegation in the genus Pelargonium. Curr Genet 5:245–249

    CAS  Google Scholar 

  • Millen RS, Olmstead RG, Adams KL, Palmer JD, Lao NT, Heggie L, Kavanagh TA, Hibberd JM, Gray JC, Morden CW, Calie PJ, Jermlin LS, Wolfe KH (2001) Many parallel losses of infA from chloroplast DNA during angiosperm evolution with multiple independent transfers to the nucleus. Plant Cell 13:645–658

    PubMed  CAS  Google Scholar 

  • Milligan BG, Hampton JN, Palmer JD (1989) Dispersed repeats and structural reorganization in subclover chloroplast DNA. Mol Biol Evol 6:355–368

    PubMed  CAS  Google Scholar 

  • Mogensen HL (1996) The hows and whys of cytoplasmic inheritance in seed plants. Am J Bot 83:383–404

    Google Scholar 

  • Moore MJ, Bell CD, Soltis PS, Soltis DE (2007) Using plastid genome-scale data to resolve enigmatic relationships among basal angiosperms. Proc Natl Acad Sci USA 104:19363–19368

    PubMed  Google Scholar 

  • Moore MJ, Soltis PS, Bell CD, Burleigh JG, Soltis DE (2010) Phylogenetic analysis of 83 plastid genes further resolves the early diversification of eudicots. Proc Natl Acad Sci USA 107:4623–4628

    PubMed  CAS  Google Scholar 

  • Morton BR (1993) Chloroplast DNA codon use: evidence for selection at the psbA locus based on tRNA availability. J Mol Evol 37:273–280

    PubMed  CAS  Google Scholar 

  • Morton BR (1994) Codon use and the rate of divergence of land plant chloroplast genes. Mol Biol Evol 11:231–238

    PubMed  CAS  Google Scholar 

  • Morton BR (1998) Selection on the codon bias of chloroplast and cyanelle genes in different plant and algal lineages. J Mol Evol 46:449–459

    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 

  • Mrácek J (2005) Investigation of interspecific genome-plastome incompatibility in Oenothera and Passiflora. PhD dissertation, University of Munich, Germany

    Google Scholar 

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

    PubMed  Google Scholar 

  • Nock C, Waters D, Edwards M, Bowen W, Rice N, Cordeiro G, Henry R (2010) Chloroplast genome sequences from total DNA for exploring plant relationships. Plant Biotechnol J. doi:10.1111/j.1467-7652.2010.00558.x

  • 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

    PubMed  CAS  Google Scholar 

  • Odintsova MS, Yurina NP (2003) Plastid genomes of higher plants and algae: structure and functions. Mol Biol 37:649–662

    CAS  Google Scholar 

  • Ohba K, Iwakawa M, Ohada Y, Murai M (1971) Paternal transmission of a plastid anomaly in some reciprocal crosses of Suzi, Cryptomeria japonica D. Don. Silvae Genet 210:101–107

    Google Scholar 

  • Ohyama K, Fukuzawa H, Kohchi T, Shirai H, Sano T, Sano S, Umesono K, Shiki Y, Takeuchi M, Chang Z, Aota S, 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 

  • Oldenburg DJ, Bendich AJ (2004) Changes in the structure of DNA molecules and the amount of DNA per plastid during chloroplast development in maize. J Mol Biol 344:1311–1330

    PubMed  CAS  Google Scholar 

  • Olmstead RG, Reeves PA, Yen AC (1998) Patterns of sequence evolution and implications for parsimony analysis of chloroplast DNA. In: Soltis DE, Soltis PS, Doyle JJ (eds) Molecular systematics of plants II: DNA sequencing. Kluwer Academic, Norwell, pp 164–187

    Google Scholar 

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

    CAS  Google Scholar 

  • Palmer JD (1991) Plastid chromosomes: structure and evolution. In: Hermann RG (ed) The molecular biology of plastids. Cell culture and somatic cell genetics of plants. Springer, Vienna, pp 5–53

    Google Scholar 

  • Palmer JD, Stein DB (1986) Conservation of chloroplast genome structure among vascular plants. Curr Genet 10:823–833

    CAS  Google Scholar 

  • Palmer JD, Aldrich J, Thompson WF (1987) Chloroplast DNA evolution among legumes: loss of a large inverted repeat occurred prior to other sequence rearrangements. Curr Genet 11:275–286

    CAS  Google Scholar 

  • Palmer JD, Osorio B, Thompson WF (1988) Evolutionary significance of inversions in legume chloroplast DNAs. Curr Genet 14:65–74

    CAS  Google Scholar 

  • Pandey K, Grant J, Williams E (1987) Interspecific hybridisation between Trifolium repens and T. uniflorum. Aust J Bot 35:171–182

    Google Scholar 

  • Parkinson CL, Mower JP, Qiu Y-Q, Shirk AJ, Song K, Young ND, de Pamphilis CW, Palmer JD (2005) Multiple major increases and decreases in mitochondrial substitution rates in the plant family Geraniaceae. BMC Evol Biol 5:73

    PubMed  Google Scholar 

  • Parks M, Cronn R, Liston A (2009) Increasing phylogenetic resolution at low taxonomic levels using massively parallel sequencing of chloroplast genomes. BMC Biol 7:84

    PubMed  Google Scholar 

  • Perry AS, Wolfe KH (2002) Nucleotide substitution rates in legume chloroplast DNA depend on the presence of the inverted repeat. J Mol Evol 55:501–508

    PubMed  CAS  Google Scholar 

  • Perry AS, Brennan S, Murphy DJ, Kavanagh TA, Wolfe KH (2002) Evolutionary re-organization of a large operon in Adzuki Bean chloroplast DNA caused by inverted repeat movement. DNA Res 9:157–162

    PubMed  CAS  Google Scholar 

  • Raubeson LA, Jansen RK (1992a) A rare chloroplast-DNA structural mutation is shared by all conifers. Biochem Syst Ecol 20:17–24

    CAS  Google Scholar 

  • Raubeson LA, Jansen RK (1992b) Chloroplast DNA evidence on the ancient evolutionary split in vascular land plants. Science 255:1697–1699

    PubMed  CAS  Google Scholar 

  • Raubeson LA, Jansen RK (2005) Chloroplast genomes of plants. In: Henry RJ (ed) Plant diversity and evolution: genotypic and phenotypic variation in higher plants. CABI, Cambridge, MA, pp 45–68

    Google Scholar 

  • Raubeson LA, Peery R, Chumley TW, Dziubek C, Fourcade HM, Boore JL, Jansen RK (2007) Comparative chloroplast genomics: analyses including new sequences from the angiosperms Nuphar advena and Ranunculus macranthus. BMC Genomics 8:174

    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 

  • Rogalski M, Ruf S, Bock R (2006) Tobacco plastid ribosomal protein S18 is essential for cell survival. Nucleic Acids Res 34:4537–4545

    PubMed  CAS  Google Scholar 

  • Rowan BA, Oldenburg DJ, Bendich AJ (2010) RecA maintains the integrity of chloroplast DNA molecules in Arabidopsis. J Exp Bot 61:2575–2588

    PubMed  CAS  Google Scholar 

  • Ruhlman T, Lee S-B, Jansen RK, Hostetler JB, Tallon LJ, Town CD, Daniell H (2006) Complete chloroplast genome sequence of Daucus carota: implications for biotechnology and phylogeny of angiosperms. BMC Genomics 7:222

    PubMed  Google Scholar 

  • Ruhlman T, Verma D, Samson N, Daniell H (2010) The role of heterologous chloroplast sequence elements in transgene integration and expression. Plant Physiol 152:2088–2104

    PubMed  CAS  Google Scholar 

  • Saski C, Lee S-B, Fjellheim S, Guda C, Jansen RK, Luo H, Tomkins J, Rognli OA, Daniell H, Clarke JL (2007) Complete chloroplast genome sequences of Hordeum vulgare, Sorghum bicolor and Agrostis stolonifera and comparative analyses with other grass genomes. Theor Appl Genet 115:571–590

    PubMed  CAS  Google Scholar 

  • Shao R, Dowton M, Murrell A, Barker SC (2003) Rates of gene rearrangement and nucleotide substitution are correlated in the mitochondrial genomes of insects. Mol Biol Evol 20:1612–1619

    PubMed  CAS  Google Scholar 

  • Shaver JM, Oldenburg DJ, Bendich AJ (2006) The structure of chloroplast DNA molecules and the effects of light on the amount of chloroplast DNA during development in Medicago truncatula. Plant Physiol 146:1064–1074

    Google Scholar 

  • Shaw J, Lickey EB, Schilling EE, Small RL (2007) Comparison of whole chloroplast genome sequences to choose noncoding regions for phylogenetic studies in angiosperms: the tortoise and the hare III. Am J Bot 94:275–288

    PubMed  CAS  Google Scholar 

  • Shimada H, Sugiura M (1991) Fine-structural features of the chloroplast genome – comparison of the sequenced chloroplast genomes. Nucleic Acids Res 19:983–995

    PubMed  CAS  Google Scholar 

  • Shinozaki K, Ohme M, Tanaka M, Wakasugi T, Hayashida N, Matsubayashi T, Zaita N, Chunwongse J, Obokata J, Yamaguchishinozaki K, Ohto C, Torazawa K, Meng BY, Sugita M, Deno H, Kamogashira T, Yamada K, Kusuda J, Takaiwa F, Kato A, Tohdoh N, Shimada H, Sugiura M (1986) The complete nucleotide-sequence of the tobacco chloroplast genome – its gene organization and expression. EMBO J 5:2043–2049

    PubMed  CAS  Google Scholar 

  • Snijder RC, Brown FS, van Tuyk JM (2007) The role of plastome-genome incompatibility and biparental plastid inheritance in interspecific hybrids in the genus Zantedeschia (Araceae). Floricul Ornam Biotechnol 1:150–157

    Google Scholar 

  • Soliman K, Fedak G, Allard RW (1987) Inheritance of organelle DNA in barley and Hordeum X Secale intergeneric hybrids. Genome 29:867–872

    CAS  Google Scholar 

  • Szmidt AE, Alden T, Hallgren JE (1987) Paternal inheritance of chloroplast DNA in Larix. Plant Mol Biol 9:59–64

    CAS  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 

  • Timme RE, Kuehl JV, Boore JL, Jansen RK (2007) A comparison of the first two sequenced chloroplast genomes in Asteraceae: Lettuce and Sunflower. Am J Bot 94:302–312

    PubMed  CAS  Google Scholar 

  • Timmis JN, Ayliffe MA, Huang CY, Martin W (2004) Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes. Nat Rev Genet 5:123–135

    PubMed  CAS  Google Scholar 

  • Tsudzuki J, Nakashima K, Tsudzuki T, Hiratsuka J, Shibata M, Wakasugi T, Sugiura M (1992) Chloroplast DNA of black pine retains a residual inverted repeat lacking rRNA genes: nucleotide sequences of trnQ, trnK, psbA, trnI and trnH and the absence of rps16. Mol Gen Genet 232:206–214

    PubMed  CAS  Google Scholar 

  • Ueda M, Fujimoto M, Arimura S-I, Murata J, Tsutsumi N, Kadowaki K-I (2007) Loss of the rpl32 gene from the chloroplast genome and subsequent acquisition of a preexisting transit peptide within the nuclear gene in Populus. Gene 402:51–56

    PubMed  CAS  Google Scholar 

  • Ueda M, Fujimoto M, Takanashi H, Arimura S-I, Tsutsumi N, Kadowaki K-I (2008) Substitution of the gene for chloroplast rps16 was assisted by generation of dual targeting signal. Mol Biol Evol 25:1566–1575

    PubMed  CAS  Google Scholar 

  • Wakasugi T, Tsudzuki J, Ito S, Nakashima K, Tsudzuki T, Sugiura M (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

    PubMed  CAS  Google Scholar 

  • Wall DP, Herbeck JT (2003) Evolutionary patterns of codon usage in the chloroplast gene rbcL. J Mol Evol 56:673–688

    PubMed  CAS  Google Scholar 

  • Wojciechowski MF, Lavin M, Sanderson MJ (2004) A phylogeny of legumes (Leguminosae) based on analysis of the plastid matK gene resolves many well supported subclades within the family. Am J Bot 91:1846–1862

    PubMed  CAS  Google Scholar 

  • Wolf PG, Der JP, Duffy AM, Davidson JB, Grusz AL, Pryer KM (2011) The evolution of chloroplast genes and genomes in ferns. Plant Mol Biol 76:251–261

    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 

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

    PubMed  CAS  Google Scholar 

  • Wu CS, Wang YN, Liu SM, Chaw SM (2007) Chloroplast genome (cpDNA) of Cycas taitungensis and 56 cp protein-coding genes of Gnetum parvifolium: insights into cpDNA evolution and phylogeny of extant seed plants. Mol Biol Evol 24:1366–1379

    PubMed  CAS  Google Scholar 

  • Wu CS, Lai YT, Lin CP, Wang YN, Chaw SM (2009) Evolution of reduced and compact chloroplast genomes (cpDNAs) in gnetophytes: selection toward a lower-cost strategy. Mol Phylogenet Evol 52:115–124

    PubMed  CAS  Google Scholar 

  • Xu W, Jameson D, Tang B, Higgs PG (2006) The relationship between the rate of molecular evolution and the rate of genome rearrangement in animal mitochondrial genomes. J Mol Evol 63:375–392

    PubMed  CAS  Google Scholar 

  • Yamane K, Yano K, Kawahara T (2006) Pattern and rate of indel evolution from whole chloroplast intergenic regions in sugarcane, maize and rice. DNA Res 13:197–204

    PubMed  CAS  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 87:1452–1458

    PubMed  CAS  Google Scholar 

  • Young ND, dePamphilis CW (2000) Purifying selection detected in the plastid gene matK and flanking ribozyme regions within a group II intron of nonphotosynthetic plants. Mol Biol Evol 17:1933–1941

    PubMed  CAS  Google Scholar 

  • Young ND, dePamphilis CW (2005) Rate variation in parasitic plants: correlated and uncorrelated patterns among plastid genes of different function. BMC Evol Biol 5:16

    PubMed  Google Scholar 

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

    PubMed  Google Scholar 

  • Zhang Q, Liu Y, Sodmergen (2003) Examination of the cytoplasmic DNA in male reproductive cells to determine the potential for cytoplasmic inheritance in 295 angiosperm species. Plant Cell Physiol 44:941–951

    PubMed  CAS  Google Scholar 

  • Zhong BJ, Yonezawa T, Zhong Y, Hasegawa M (2009) Episodic evolution and adaptation of chloroplast genomes in ancestral grasses. PLoS One 4:e5297

    PubMed  Google Scholar 

  • Zhong B, Yonezawa T, Zhong Y, Hasegawa M (2010) The position of Gnetales among seed plants: overcoming pitfalls of chloroplast phylogenomics. Mol Biol Evol 27:2855–2863

    PubMed  CAS  Google Scholar 

Download references

Acknowledgments

Support was provided by the National Science Foundation (DEB-0717372 to RKJ and IOS-1027259 to RKJ and TAR) and the Fred G. Gloeckner Foundation (to TAR and RKJ). The authors thank J. Chris Blazier and Mao-Lun Weng for comments on an earlier version of the manuscript.

Author information

Authors and Affiliations

  1. Section of Integrative Biology, University of Texas at Austin, 1 University Station C0930, Austin, TX, 78712, USA

    Robert K. Jansen & Tracey A. Ruhlman

  2. Department of Biological Sciences, Genomics and Biotechnology Section, King Abdulaziz University, Jeddah, 21589, Saudi Arabia

    Robert K. Jansen & Tracey A. Ruhlman

Authors
  1. Robert K. Jansen
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tracey A. Ruhlman
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Robert K. Jansen .

Editor information

Editors and Affiliations

  1. AM MUEHLENBERG 1, POTSDAM-GOLM 14476, Germany

    Ralph Bock

  2. Inst. Zelluläre und Molekulare, Botanik (IZMB), Universität Bonn, Kirschallee 1, Bonn, 53115, Germany

    Volker Knoop

Rights and permissions

Reprints and permissions

Copyright information

© 2012 Springer Science+Business Media B.V.

About this chapter

Cite this chapter

Jansen, R.K., Ruhlman, T.A. (2012). Plastid Genomes of Seed Plants. In: Bock, R., Knoop, V. (eds) Genomics of Chloroplasts and Mitochondria. Advances in Photosynthesis and Respiration, vol 35. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-2920-9_5

Download citation

Publish with us

Policies and ethics

Search

Navigation