Current Genetics

, Volume 52, Issue 5–6, pp 267–274 | Cite as

OrganellarGenomeDRAW (OGDRAW): a tool for the easy generation of high-quality custom graphical maps of plastid and mitochondrial genomes

  • Marc Lohse
  • Oliver Drechsel
  • Ralph BockEmail author
Technical Note


Mitochondria and plastids are DNA-containing cell organelles whose genomes occur at high copy numbers per cell. Organellar genomes vary greatly in size ranging from approximately 15 kb for some animal mitochondrial genomes to more than 2 Mb for some plant mitochondrial genomes. The vast majority of organellar genomes map as circular molecules that are difficult to illustrate by available commercial or free software tools. Thus, published genome maps are extremely heterogeneous in design, often tediously drawn semi-manually and lack any consensus in display. Here, we present a new web-based tool, OrganellarGenomeDRAW (OGDRAW), which produces high-resolution custom graphical maps of DNA sequences as stored in standard GenBank format entries. GenBank data can be provided as either file uploads or accession numbers. The program is specially optimized for the display of chloroplast and mitochondrial genomes but can also be used to depict other circular DNA sequences. The design of the program core as a Perl module with an object-oriented interface allows easy integration into custom scripts.


Plastid Mitochondrion Physical map Restriction map Bioinformatics Software tool 



We thank Peter Krüger (MPI-MP) for server set-up and administration and many helpful comments on the design of the website. We are grateful to the members of the Bock laboratory for critical testing of OGDRAW and useful suggestions. We wish to acknowledge the creators and contributors to the BioPerl and ImageMagick projects for providing excellent free software tools. This research was supported by grants from the European Union (FP6 Plastomics project LSHG-CT-2003-503238) and by the Max Planck Society.


  1. Anderson S, Bankier AT, Barrell BG, de Bruijn MHL, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJH, Staden R, Young IG (1981) Sequence and organization of the human mitochondrial genome. Nature 290:457–464PubMedCrossRefGoogle Scholar
  2. Backert S, Nielsen BL, Börner T (1997) The mystery of the rings: structure and replication of mitochondrial genomes from higher plants. Trends Plant Sci 2:477–483CrossRefGoogle Scholar
  3. Bock R (2007) Structure, function, and inheritance of plastid genomes. Top Curr Genet 20:29–63Google Scholar
  4. Bungard RA (2004) Photosynthetic evolution in parasitic plants: insight from the chloroplast genome. Bioessays 26:235–247PubMedCrossRefGoogle Scholar
  5. Burland TG (2000) DNASTAR’s Lasergene sequence analysis software. Methods Mol Biol 132:71–91PubMedGoogle Scholar
  6. Chumley TW, Palmer JD, Mower JP, Fourcade HM, Calie PJ, Boore JL, Jansen RK (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 23:2175–2190PubMedCrossRefGoogle Scholar
  7. dePamphilis CW, Palmer JD (1990) Loss of photosynthetic and chlororespiratory genes from the plastid genome of a parasitic flowering plant. Nature 348:337–339PubMedCrossRefGoogle Scholar
  8. Dong X, Stothard P, Forsythe IJ, Wishart DS (2004) PlasMapper: a web server for drawing and auto-annotating plasmid maps. Nucleic Acids Res 32:W660–W664PubMedCrossRefGoogle Scholar
  9. 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 48:236–244PubMedCrossRefGoogle Scholar
  10. Gray MW, Lang BF, Cedergren R, Golding GB, Lemieux C, Sankoff D, Tumel M, Brossard N, Delage E, Littlejohn TG, Plante I, Rioux P, Saint-Louis D, Zhu Y, Burger G (1998) Genome structure and gene content in protist mitochondrial DNAs. Nucleic Acids Res 26:865–878PubMedCrossRefGoogle Scholar
  11. Knoop V (2004) The mitochondrial DNA of land plants: peculiarities in phylogenetic perspective. Curr Genet 46:123–139PubMedCrossRefGoogle Scholar
  12. Lang BF, Burger G, O’Kelly CJ, Cedergren R, Golding GB, Lemieux C, Sankoff D, Turmel M, Gray MW (1997) An ancestral mitochondrial DNA resembling a eubacterial genome in miniature. Nature 387:493–497PubMedCrossRefGoogle Scholar
  13. Lu G, Moriyama EN (2004) Vector NTI, a balanced all-in-one sequence analysis suite. Brief Bioinform 5:378–388PubMedCrossRefGoogle Scholar
  14. Maul JE, Lilly JW, Cui L, dePamphilis CW, Miller W, Harris EH, Stern DB (2002) The Chlamydomonas reinhardtii plastid chromosome: islands of genes in a sea of repeats. Plant Cell 14:2659–2679PubMedCrossRefGoogle Scholar
  15. Ohyama K, Fukuzawa H, Kohchi T, Shirai H, Sano T, Sano S, Umesono K, Shiki Y, Takeuchi M, Chang Z, Aota S-i, Inokuchi H, Ozeki H (1986) Chloroplast gene organization deduced from complete sequence of liverwort Marchantia polymorpha chloroplast DNA. Nature 322:572–574CrossRefGoogle Scholar
  16. Palmer JD, Nugent JM, Hebron LA (1987) Unusual structure of geranium chloroplast DNA: a triple-sized inverted repeat, extensive gene duplications, multiple inversions, and two repeat families. Proc Natl Acad Sci USA 84:769–773PubMedCrossRefGoogle Scholar
  17. Shinozaki K, Ohme M, Tanaka M, Wakasugi T, Hayashida N, Matsubayashi T, Zaita N, Chunwongse J, Obokata J, Yamaguchi-Shinozaki 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 5:2043–2049PubMedGoogle Scholar
  18. Stothard P, Wishart DS (2005) Circular genome visualization and exploration using CGView. Bioinformatics 21:537–539PubMedCrossRefGoogle Scholar
  19. Tsudzuki T (2000) A graphic tool for circular genome maps. Nucleic Acids Symp Ser 44:189–190PubMedGoogle Scholar
  20. Unseld M, Marienfeld JR, Brandt P, Brennicke A (1997) The mitochondrial genome of Arabidopsis thaliana contains 57 genes in 366,924 nucleotides. Nat Genet 15:57–61PubMedCrossRefGoogle Scholar
  21. Wakasugi T, Tsudzuki T, Sugiura M (2001) The genomics of land plant chloroplasts: gene content and alteration of genomic information by RNA editing. Photosynth Res 70:107–118PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2007

Authors and Affiliations

  1. 1.Max-Planck-Institut für Molekulare PflanzenphysiologiePotsdam-GolmGermany

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