Skip to main content

Part of the book series: Biotechnology Intelligence Unit ((BIOIU))

Abstract

This review summarizes recent data from chloroplast genomics research, namely the structure and gene content in completely sequenced chloroplast genomes of land plants and algae. It aims to highlight the structural similarity of chloroplast DNAs (cpDNA) gene content and arrangement in various lineages of land plants. It is noteworthy that chloroplast genomes of algae show significantly less structural similarity than those of land plants. Algae contain several unique genes, which are not found in cpDNAs of land plants. The organization of genes on the plastid chromosome differs drastically in land plants and algae. The problems of origin and evolution of plastids are briefly discussed.

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

Access this chapter

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

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Leister D. Chloroplast research in the genomic age. Trends in Genetics 2003; 19:47–56.

    Article  PubMed  CAS  Google Scholar 

  2. Raven JA, Allen JF. Genomics and chloroplast evolution: What did cyanobacteria do for plants? Genome Biology 2003; 4:209.1–209.5.

    Article  Google Scholar 

  3. Wakasugi T, Tsudzuki T, Sugiura M. The genomics of land plant chloroplasts: Gene content and alteration of genomic information by RNA editing. Photosynthesis Res 2001; 70:107–118.

    Article  CAS  Google Scholar 

  4. Cosner ME, Jansen RK, Palmer JD et al. 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 1997; 31:419–429.

    Article  PubMed  CAS  Google Scholar 

  5. Lilly JW, Havey MJ, Jackson SA et al. Cytogenomic analyses reveal the structural plasticity of the chloroplast genome in land plants. The Plant Cell 2001; 13:245–254.

    Article  PubMed  CAS  Google Scholar 

  6. Shinozaki K, Ohme M, Tanaka M et al. The complete nucleotide sequence of the tobacco chloroplast genome: Its gene organization and expression. EMBO J 1986; 5:2043–2049.

    PubMed  CAS  Google Scholar 

  7. Ohyama K, Fukuzawa H, Kohchi T et al. Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA. Nature 1986; 322:572–574.

    Article  CAS  Google Scholar 

  8. Hiratsuka J, Shimada H, Whittier R et al. 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 1989; 217:185–194.

    Article  PubMed  CAS  Google Scholar 

  9. Ogihara Y, Isono K, Kojima T et al. Structural features of a wheat plastome as revealed by complete sequencing of chloroplast DNA. Mol Genet Genomics 2002; 266:740–746.

    Article  PubMed  CAS  Google Scholar 

  10. Sugiura M, Hirose T, Sugita M. Evolution and mechanism of translation in chloroplasts. Annu Rev Genetics 1998; 32:437–459.

    Article  CAS  Google Scholar 

  11. Sato S, Nakamura Y, Kaneko T et al. Complete structure of the chloroplast genome of Arabidopsis thaliana. DNA Res 1999; 6:283–290.

    Article  PubMed  CAS  Google Scholar 

  12. Kato T, Kaneko T, Sato S et al. Complete structure of the chloroplast genome of a legume, Lotus japonicus. DNA Res 2000; 7:323–330.

    Article  PubMed  CAS  Google Scholar 

  13. Knox EB, Palmer JD. The chloroplast genome arrangement of Lobelia thuliniana (Lobeliaceae): Expansion of the inverted repeat in an ancestor of the Campanulales. Pl Syst Evol 1999; 214:49–64.

    Article  Google Scholar 

  14. Hupfer H, Swiatek M, Hornung S et al. Complete nucleotide sequence of the Oenothera elata plastid chromosome, representing plastome I of the five distinguishable Euoenothera plastomes. Mol Gen Genet 2000; 263:581–585.

    PubMed  CAS  Google Scholar 

  15. Schmitz-Linneweber CH, Maier R, Alcaraz JP et al. The plastid chromosome of spinach (Spinacia oleracea): Complete nucleotide sequence and gene organization. Plant Mol Biol 2001; 45:307–315.

    Article  PubMed  CAS  Google Scholar 

  16. Katayama H, Ogihara Y. Structural alterations of the chloroplast genome found in grasses are not common in monocots. Curr Genet 1993; 23:160–165.

    Article  PubMed  CAS  Google Scholar 

  17. Maier RM, Neckermann K, Igloi GL et al. Complete sequence of the maize chloroplast genome: Gene content, hotspots of divergence and fine tuning of genetic information by transcript editing. J Mol Biol 1995; 251:614–628.

    Article  PubMed  CAS  Google Scholar 

  18. Douglas SE. Chloroplast origins and evolution. In: Bryant A, ed. The Molecular Biology of Cyanobacteria. Amsterdam: Kluwer, 1994:91–118.

    Google Scholar 

  19. Wakasugi T, Sugita M, Tsudzuki T et al. Updated gene map of tobacco chloroplast DNA. Plant Mol Biol Rep 1998; 16:231–241.

    Article  CAS  Google Scholar 

  20. Kowallik KV. Origin and evolution of chloroplasts: Current status and future perspectives. In: Schenk H, Herrmann RG, Jeon KW et al, eds. Eukaryotism and Symbiosis. Intertaxonic Combination versus Symbiotic Adaptation. Berlin: Springer, 1997:3–23.

    Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  22. Bommer D, Haberhausen G, Zetsche K. A large deletion in the plastid DNA of the holoparasitic flowering plant Cuscuta reflexa concerning two ribosomal proteins (rpl2, rpl23), one transfer RNA (trnI) and an ORF2280 homologue. Curr Genet 1993; 24:171–176.

    Article  PubMed  CAS  Google Scholar 

  23. Odintsova MS, Yurina NP. RNA editing in chloroplasts and plant mitochondria. Genetika 2000; 37:307–320.

    Google Scholar 

  24. Schmitz-Linneweber C, Regel R, Du TG et al. 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 2002; 19:1602–1612.

    PubMed  CAS  Google Scholar 

  25. Wakasugi T, Nagai M, Kapoor M et al. 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 1997; 94:5967–5972.

    Article  PubMed  CAS  Google Scholar 

  26. Turmel M, Otis CH, Lemieux C. The complete chloroplast DNA sequence of the green alga Nephroselmis olivacea: Insights into the architecture of ancestral chloroplast genomes. Proc Natl Acad Sci USA 1999; 96:10248–10253.

    Article  PubMed  CAS  Google Scholar 

  27. Sugiura M. The discovery of the complete sequence of tobacco and rice chloroplast genomes. In: Kung S-D, Yang S-F, eds. Discoveries in Plant Biology, Vol. 2. Singapore: World Scientific, 1998:45–60.

    Google Scholar 

  28. Freyer R, Neckermann K, Maier RM et al. Structural and functional analysis of plastid genomes from parasitic plants: Loss of an intron within the genus Cuscuta. Curr Genet 1995; 27:580–586.

    Article  PubMed  CAS  Google Scholar 

  29. Wakasugi T, Tsudzuki J, Ito S et al. Loss of all ndh genes as determined by sequencing the entire chloroplast genome of the black pine Pinus thunbergii. Proc Natl Acad Sci USA 1994; 91:9794–9798.

    Article  PubMed  CAS  Google Scholar 

  30. Millen RS, Olmstead RG, Adams KL et al. Many parallel losses of infA from chloroplast DNA during angiosperm evolution with multiple independent transfers to the nucleus. Plant Cell 2001; 13:645–658.

    Article  PubMed  CAS  Google Scholar 

  31. Guera A, De Nova PG, Sabater B. Identification of the Ndh(NAD(P)H-plastoquinone-oxidoreductase) complex in etioplast membranes of barley: Changes during photomorphogenesis of chloroplasts. Plant Cell Physiol 2000; 41:49–59.

    PubMed  CAS  Google Scholar 

  32. Stoebe B, Martin W, Kowallik KV. Distribution and nomenclature of protein-coding genes in 12 sequenced chloroplast genomes. Plant Mol Biol Rep 1998; 16:243–255.

    Article  CAS  Google Scholar 

  33. Bhattacharya D, Medlin L. Algal phylogeny and the origin of land plants. Plant Physiol 1998; 116:9–15.

    Article  CAS  Google Scholar 

  34. Douglas SE. Plastid evolution: Origins, diversity, trends. Curr Opin Genet Dev 1998; 8:655–661.

    Article  PubMed  CAS  Google Scholar 

  35. Palmer JD. A single birth of all plastids? Nature 2000; 405:32–33.

    Article  PubMed  CAS  Google Scholar 

  36. Simpson CL, Stern DB. The treasure trove of algal chloroplast genomes. Surprises in architecture and gene content, and their functional implications. Plant Physiol 2002; 129:957–966.

    Article  PubMed  CAS  Google Scholar 

  37. Kaneko T, Sato S, Kotani H et al. Sequence analysis of the genome of the unicellular cyanobacterium Synechocystis sp. strain PCC 6803. II. Sequence determination of the entire genome and assignment of potential protein-coding regions. DNA Res 1996; 3:109–136.

    Article  PubMed  CAS  Google Scholar 

  38. Maul JE, Lilly JW, Liying Cui et al. The Chlamydomonas reinhardtii plastid chromosome. Islands of genes in a sea of repeats. The Plant Cell 2002; 14:2659–2679.

    Article  PubMed  CAS  Google Scholar 

  39. Hallick RB, Hong L, Drager RG et al. Complete sequence of Euglena gracilis chloroplast DNA. Nucl Acids Res 1993; 21:3537–3544.

    Article  PubMed  CAS  Google Scholar 

  40. Gockel G, Hachtel W. Complete gene map of the plastid genome of the nonphotosynthetic euglenoid flagellate Astasia longa. Protist 2000; 151:347–351.

    Article  PubMed  CAS  Google Scholar 

  41. Zhang Z, Green BR, Cavalier-Smith T. Single gene circles in dinoflagellate chloroplast genomes. Nature 1999; 400:155–159.

    Article  PubMed  CAS  Google Scholar 

  42. Glockner G, Rosenthal A, Valentin K. The structure and gene repertoire of an ancient red algal plastid genome. J Mol Evol 2000; 51:382–390.

    PubMed  CAS  Google Scholar 

  43. Lemieux CX, Otis CH, Turmel M. Ancestral chloroplast genome in Mesostigma viride reveals an early branch of green plant evolution. Nature 2000; 403:649–652.

    Article  PubMed  CAS  Google Scholar 

  44. Turmel M, Otis C, Lemieux C. 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 2002; 99(17):11275–11280.

    Article  PubMed  CAS  Google Scholar 

  45. Douglas SE, Penny SL. 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 1999; 48:236–244.

    Article  PubMed  CAS  Google Scholar 

  46. Reith M, Munholland J. Complete nucleotide sequence of the Porphyra purpurea chloroplast genome. Plant Mol Biol Rep 1995; 13:333–335.

    CAS  Google Scholar 

  47. Baum M, Cordier A, Schon A. RNase P from a photosynthetic organelle contains an RNA homologous to the cyanobacterial counterpart. J Mol Biol 1996; 257:43–52.

    Article  PubMed  CAS  Google Scholar 

  48. Stirewalt VL, Michalowski CB, Löffelhardt W et al. Nucleotide sequence of the cyanelle genome from Cyanophora paradoxa. Plant Mol Biol Rep 1995; 13:327–332.

    CAS  Google Scholar 

  49. Ebel C, Frantz C, Paulus F et al. Trans-splicing and cis-splicing in the colourless euglenoid, Entosiphon sulcatum. Curr Genet 1999; 35:542–550.

    Article  PubMed  CAS  Google Scholar 

  50. Osteryoung KW. Organelle fission. Crossing the evolutionary divide. Plant Physiol 2000; 123:1213–1216.

    Article  PubMed  CAS  Google Scholar 

  51. Ohta N, Sato N, Kuroiwa T. Analysis of the plastid genome of protoflorideophyceous algae Cyanidioschizon merolae. Plant Cell Physiol 1998; 39(Suppl 01):54.

    Google Scholar 

  52. Martin W, Stoebe B, Goremykin V et al. Gene transfer to the nucleus and the evolution of chloroplasts. Nature 1998; 393:162–165.

    Article  PubMed  CAS  Google Scholar 

  53. Zerges W. Does complexity constrain organelle evolution? Trends in Plant Sci 2002; 7(4):175–181.

    Article  CAS  Google Scholar 

  54. Douglas AE, Raven JA. Genomes at the interface between bacteria and organelles. Phil Trans R Soc Lond B 2003; 358:5–18.

    Article  CAS  Google Scholar 

  55. Martin W, Herrmann RG. Gene transfer from organelles to the nucleus: How much, what happens, and why? Plant Physiol 1998; 118:9–17.

    Article  PubMed  CAS  Google Scholar 

  56. Doolittle WF, Boucher Y, Nesbo CL et al. How big is the iceberg of which organellar genes in nuclear genomes are but the tip? Phil Trans. R Soc Lond B 2003; 358:39–57.

    Article  CAS  Google Scholar 

  57. Stegemann S, Hartmann S, Ruf S et al. High-frequency gene transfer from the chloroplast genome to the nucleus. Proc Natl Acad Sci USA 2003; 100:8828–8833.

    Article  PubMed  CAS  Google Scholar 

  58. Allen JF. The function of genomes in bioenergetic organelles. Phil Trans R Soc Lond B 2003; 358:19–37.

    Article  CAS  Google Scholar 

  59. Steiner JM, Löffelhardt W. Protein import into cyanelles. Trends in Plant Sci 2002; 7:72–77.

    Article  CAS  Google Scholar 

  60. Martin W, Rujan T, Richly E et al. Evolutionary analysis of Arabidopsis, cyanobacterial, and chloroplast genomes reveals plastid phylogeny and thousands of cyanobacterial genes in the nucleus. Proc Natl Acad Sci USA 2002; 99:12246–12251.

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Nadezhda P. Yurina .

Rights and permissions

Reprints and permissions

Copyright information

© 2006 Landes Bioscience

About this chapter

Cite this chapter

Odintsova, M.S., Yurina, N.P. (2006). Chloroplast Genomics of Land Plants and Algae. In: Biotechnological Applications of Photosynthetic Proteins: Biochips, Biosensors and Biodevices. Biotechnology Intelligence Unit. Springer, Boston, MA. https://doi.org/10.1007/978-0-387-36672-2_6

Download citation

Publish with us

Policies and ethics