OpenLB
Open Library of Bioscience
Advanced Search
Nature genetics
Feb, 2011;43 (2): 101-8.

The genome of Theobroma cacao.

Xavier Argout, Jerome Salse, Jean-Marc Aury, Mark J Guiltinan, Gaetan Droc, Jerome Gouzy, Mathilde Allegre, Cristian Chaparro, Thierry Legavre, Siela N Maximova, Michael Abrouk, Florent Murat, Olivier Fouet, Julie Poulain, Manuel Ruiz, Yolande Roguet, Maguy Rodier-Goud, Jose Fernandes Barbosa-Neto, Francois Sabot, Dave Kudrna, Jetty Siva S Ammiraju, Stephan C Schuster, John E Carlson, Erika Sallet, Thomas Schiex, Anne Dievart, Melissa Kramer, Laura Gelley, Zi Shi, Aurélie Bérard, Christopher Viot, Michel Boccara, Ange Marie Risterucci, Valentin Guignon, Xavier Sabau, Michael J Axtell, Zhaorong Ma, Yufan Zhang, Spencer Brown, Mickael Bourge, Wolfgang Golser, Xiang Song, Didier Clement, Ronan Rivallan, Mathias Tahi, Joseph Moroh Akaza, Bertrand Pitollat, Karina Gramacho, Angélique D'Hont, Dominique Brunel, Diogenes Infante, Ismael Kebe, Pierre Costet, Rod Wing, W Richard McCombie, Emmanuel Guiderdoni, Francis Quetier, Olivier Panaud, Patrick Wincker, Stephanie Bocs, Claire Lanaud
Author Information
  1. Xavier Argout: Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD)-Biological Systems Department-Unité Mixte de Recherche Développement et Amélioration des Plantes (UMR DAP) TA A 96/03-34398, Montpellier, France. xavier.argout@cirad.fr
PMID: 21186351 DOI: 10.1038/ng.736

Abstract

We sequenced and assembled the draft genome of Theobroma cacao, an economically important tropical-fruit tree crop that is the source of chocolate. This assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of these genes anchored on the 10 T. cacao chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example, flavonoid-related genes. It also provides a major source of candidate genes for T. cacao improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten T. cacao chromosomes were shaped from an ancestor through eleven chromosome fusions.

References

  1. Nature. 2000 Dec 14;408(6814):796-815 pubmed:11130711
  2. Mol Gen Genet. 1996 Mar 7;250(4):405-13 pubmed:8602157
  3. Heredity (Edinb). 2003 Sep;91(3):322-30 pubmed:12939635
  4. Nature. 2009 Jan 29;457(7229):551-6 pubmed:19189423
  5. Mol Plant Microbe Interact. 2008 May;21(5):507-17 pubmed:18393610
  6. Proc Natl Acad Sci U S A. 2009 Sep 1;106(35):14908-13 pubmed:19706486
  7. Nat Immunol. 2006 Dec;7(12):1243-9 pubmed:17110940
  8. Genome Res. 2010 Nov;20(11):1545-57 pubmed:20876790
  9. Nature. 2008 Apr 24;452(7190):991-6 pubmed:18432245
  10. Plant Physiol. 2003 Jun;132(2):681-97 pubmed:12805597
  11. Genome Res. 2003 Sep;13(9):2178-89 pubmed:12952885
  12. BMC Genomics. 2008 Dec 16;9:603 pubmed:19087275
  13. J Agric Food Chem. 2007 May 16;55(10):3926-35 pubmed:17439235
  14. Genes Nutr. 2009 Dec;4(4):243-50 pubmed:19685255
  15. Plant Physiol. 2009 May;150(1):12-26 pubmed:19321712
  16. Mol Biol Evol. 1994 Sep;11(5):725-36 pubmed:7968486
  17. Nature. 2007 Sep 27;449(7161):463-7 pubmed:17721507
  18. Cell. 2009 Feb 20;136(4):669-87 pubmed:19239888
  19. J Appl Genet. 2002;43(4):403-14 pubmed:12441626
  20. Planta. 1991 May;184(2):279-84 pubmed:24194081
  21. Science. 2009 Nov 20;326(5956):1112-5 pubmed:19965430
  22. PLoS Genet. 2009 Nov;5(11):e1000743 pubmed:19956743
  23. Int J Mol Sci. 2009 Nov 20;10(10):4290-309 pubmed:20057946
  24. Nature. 2010 Jan 14;463(7278):178-83 pubmed:20075913
  25. BMC Res Notes. 2009 Sep 28;2:197 pubmed:19785756
  26. BMC Plant Biol. 2010 Nov 15;10:248 pubmed:21078185
  27. Nucleic Acids Res. 2008 Jan;36(Database issue):D154-8 pubmed:17991681
  28. J Mol Evol. 2000 Mar;50(3):203-13 pubmed:10754062
  29. Planta. 2006 Sep;224(4):740-9 pubmed:16362326
  30. Cell. 2009 May 29;137(5):804-6 pubmed:19490889
  31. Bioinformatics. 2005 Apr 15;21(8):1332-8 pubmed:15564294
  32. Heredity (Edinb). 2002 Nov;89(5):380-6 pubmed:12399997
  33. Science. 2006 Sep 15;313(5793):1596-604 pubmed:16973872
  34. Trends Plant Sci. 2007 Jan;12(1):29-36 pubmed:17161643
  35. BMC Genomics. 2008 Oct 30;9:512 pubmed:18973681
  36. Proc Natl Acad Sci U S A. 2007 Nov 27;104(48):18937-40 pubmed:18024588
  37. Brief Bioinform. 2009 Nov;10(6):619-30 pubmed:19720678
  38. Biol Cell. 1993;78(1-2):41-51 pubmed:8220226
  39. Genome Res. 2006 Jan;16(1):140-7 pubmed:16344555
  40. Development. 2004 Jan;131(2):251-61 pubmed:14701679
  41. Trends Plant Sci. 2010 Sep;15(9):479-87 pubmed:20638891
  42. Science. 2008 Apr 25;320(5875):486-8 pubmed:18436778
  43. Nature. 2005 Aug 11;436(7052):793-800 pubmed:16100779
  44. Theor Appl Genet. 2004 Apr;108(6):1151-61 pubmed:14760486

MeSH Term

Cacao
Cell Nucleus
DNA
DNA Transposable Elements
Evolution, Molecular
Gene Expression Regulation, Plant
Genes, Plant
Genome, Plant
Genotype
Homozygote
In Situ Hybridization
Models, Genetic
Quantitative Trait Loci

Chemicals

DNA Transposable Elements
DNA
Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

Word Cloud