Home LiteratureArticle Details
PMID: 21186351 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't Research Support, U.S. Gov't, Non-P.H.S.

The genome of Theobroma cacao.

Nature genetics ·Vol. 43 ·No. 2 ·2011-02-00 ·Pages 101-8

Argout X, Salse J, Aury JM, Guiltinan MJ, Droc G, Gouzy J, Allegre M, Chaparro C, Legavre T, Maximova SN, Abrouk M, Murat F, Fouet O, Poulain J, Ruiz M, Roguet Y, Rodier-Goud M, Barbosa-Neto JF, Sabot F, Kudrna D, Ammiraju JS, Schuster SC, Carlson JE, Sallet E, Schiex T, Dievart A, Kramer M, Gelley L, Shi Z, Bérard A, Viot C, Boccara M, Risterucci AM, Guignon V, Sabau X, Axtell MJ, Ma Z, Zhang Y, Brown S, Bourge M, Golser W, Song X, Clement D, Rivallan R, Tahi M, Akaza JM, Pitollat B, Gramacho K, D'Hont A, Brunel D, Infante D, Kebe I, Costet P, Wing R, McCombie WR, Guiderdoni E, Quetier F, Panaud O, Wincker P, Bocs S, Lanaud C

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.

MeSH Terms
Cacao/genetics Cell Nucleus/genetics DNA/genetics 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
Authors & Affiliations
61 authors, click to expand affiliations / ORCID
Argout Xavier
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
Salse Jerome
Aury Jean-Marc
Guiltinan Mark J
Droc Gaetan
Gouzy Jerome
Allegre Mathilde
Chaparro Cristian
Legavre Thierry
Maximova Siela N
Abrouk Michael
Murat Florent
Fouet Olivier
Poulain Julie
Ruiz Manuel
Roguet Yolande
Rodier-Goud Maguy
Barbosa-Neto Jose Fernandes
Sabot Francois
Kudrna Dave
Ammiraju Jetty Siva S
Schuster Stephan C
Carlson John E
Sallet Erika
Schiex Thomas
Dievart Anne
Kramer Melissa
Gelley Laura
Shi Zi
Bérard Aurélie
Viot Christopher
Boccara Michel
Risterucci Ange Marie
Guignon Valentin
Sabau Xavier
Axtell Michael J
Ma Zhaorong
Zhang Yufan
Brown Spencer
Bourge Mickael
Golser Wolfgang
Song Xiang
Clement Didier
Rivallan Ronan
Tahi Mathias
Akaza Joseph Moroh
Pitollat Bertrand
Gramacho Karina
D'Hont Angélique
Brunel Dominique
Infante Diogenes
Kebe Ismael
Costet Pierre
Wing Rod
McCombie W Richard
Guiderdoni Emmanuel
Quetier Francis
Panaud Olivier
Wincker Patrick
Bocs Stephanie
Lanaud Claire
References (44)
44 references, click to expand
  1. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
    Nature. 2000 Dec 14;408(6814):796-815 PMID: 11130711
  2. Characterisation of the double genome structure of modern sugarcane cultivars (Saccharum spp.) by molecular cytogenetics.
    Mol Gen Genet. 1996 Mar 7;250(4):405-13 PMID: 8602157
  3. Cacao domestication II: progenitor germplasm of the Trinitario cacao cultivar.
    Heredity (Edinb). 2003 Sep;91(3):322-30 PMID: 12939635
  4. The Sorghum bicolor genome and the diversification of grasses.
    Nature. 2009 Jan 29;457(7229):551-6 PMID: 19189423
  5. Plant receptor-like serine threonine kinases: roles in signaling and plant defense.
    Mol Plant Microbe Interact. 2008 May;21(5):507-17 PMID: 18393610
  6. Reconstruction of monocotelydoneous proto-chromosomes reveals faster evolution in plants than in animals.
    Proc Natl Acad Sci U S A. 2009 Sep 1;106(35):14908-13 PMID: 19706486
  7. Plant NBS-LRR proteins in pathogen sensing and host defense.
    Nat Immunol. 2006 Dec;7(12):1243-9 PMID: 17110940
  8. Ancestral grass karyotype reconstruction unravels new mechanisms of genome shuffling as a source of plant evolution.
    Genome Res. 2010 Nov;20(11):1545-57 PMID: 20876790
  9. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).
    Nature. 2008 Apr 24;452(7190):991-6 PMID: 18432245
  10. Arabidopsis genes involved in acyl lipid metabolism. A 2003 census of the candidates, a study of the distribution of expressed sequence tags in organs, and a web-based database.
    Plant Physiol. 2003 Jun;132(2):681-97 PMID: 12805597
  11. OrthoMCL: identification of ortholog groups for eukaryotic genomes.
    Genome Res. 2003 Sep;13(9):2178-89 PMID: 12952885
  12. High quality draft sequences for prokaryotic genomes using a mix of new sequencing technologies.
    BMC Genomics. 2008 Dec 16;9:603 PMID: 19087275
  13. A new process to develop a cocoa powder with higher flavonoid monomer content and enhanced bioavailability in healthy humans.
    J Agric Food Chem. 2007 May 16;55(10):3926-35 PMID: 17439235
  14. Flavonoids and brain health: multiple effects underpinned by common mechanisms.
    Genes Nutr. 2009 Dec;4(4):243-50 PMID: 19685255
  15. Evolutionary history and stress regulation of plant receptor-like kinase/pelle genes.
    Plant Physiol. 2009 May;150(1):12-26 PMID: 19321712
  16. A codon-based model of nucleotide substitution for protein-coding DNA sequences.
    Mol Biol Evol. 1994 Sep;11(5):725-36 PMID: 7968486
  17. The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla.
    Nature. 2007 Sep 27;449(7161):463-7 PMID: 17721507
  18. Origin, biogenesis, and activity of plant microRNAs.
    Cell. 2009 Feb 20;136(4):669-87 PMID: 19239888
  19. Structure and evolution of plant disease resistance genes.
    J Appl Genet. 2002;43(4):403-14 PMID: 12441626
  20. The regulation of triacylglycerol biosynthesis in cocoa (Theobroma cacao) L.
    Planta. 1991 May;184(2):279-84 PMID: 24194081
  21. The B73 maize genome: complexity, diversity, and dynamics.
    Science. 2009 Nov 20;326(5956):1112-5 PMID: 19965430
  22. Maize centromere structure and evolution: sequence analysis of centromeres 2 and 5 reveals dynamic Loci shaped primarily by retrotransposons.
    PLoS Genet. 2009 Nov;5(11):e1000743 PMID: 19956743
  23. Polyphenols from cocoa and vascular health-a critical review.
    Int J Mol Sci. 2009 Nov 20;10(10):4290-309 PMID: 20057946
  24. Genome sequence of the palaeopolyploid soybean.
    Nature. 2010 Jan 14;463(7278):178-83 PMID: 20075913
  25. TIR-NBS-LRR genes are rare in monocots: evidence from diverse monocot orders.
    BMC Res Notes. 2009 Sep 28;2:197 PMID: 19785756
  26. Functional analysis of the Theobroma cacao NPR1 gene in Arabidopsis.
    BMC Plant Biol. 2010 Nov 15;10:248 PMID: 21078185
  27. miRBase: tools for microRNA genomics.
    Nucleic Acids Res. 2008 Jan;36(Database issue):D154-8 PMID: 17991681
  28. Divergent evolution of plant NBS-LRR resistance gene homologues in dicot and cereal genomes.
    J Mol Evol. 2000 Mar;50(3):203-13 PMID: 10754062
  29. Over-expression of a cacao class I chitinase gene in Theobroma cacao L. enhances resistance against the pathogen, Colletotrichum gloeosporioides.
    Planta. 2006 Sep;224(4):740-9 PMID: 16362326
  30. NPR1 in Plant Defense: It's Not over 'til It's Turned over.
    Cell. 2009 May 29;137(5):804-6 PMID: 19490889
  31. SpliceMachine: predicting splice sites from high-dimensional local context representations.
    Bioinformatics. 2005 Apr 15;21(8):1332-8 PMID: 15564294
  32. Cacao domestication I: the origin of the cacao cultivated by the Mayas.
    Heredity (Edinb). 2002 Nov;89(5):380-6 PMID: 12399997
  33. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray).
    Science. 2006 Sep 15;313(5793):1596-604 PMID: 16973872
  34. Flavonoid oxidation in plants: from biochemical properties to physiological functions.
    Trends Plant Sci. 2007 Jan;12(1):29-36 PMID: 17161643
  35. Towards the understanding of the cocoa transcriptome: Production and analysis of an exhaustive dataset of ESTs of Theobroma cacao L. generated from various tissues and under various conditions.
    BMC Genomics. 2008 Oct 30;9:512 PMID: 18973681
  36. Chemical and archaeological evidence for the earliest cacao beverages.
    Proc Natl Acad Sci U S A. 2007 Nov 27;104(48):18937-40 PMID: 18024588
  37. Improved criteria and comparative genomics tool provide new insights into grass paleogenomics.
    Brief Bioinform. 2009 Nov;10(6):619-30 PMID: 19720678
  38. A cytometric exercise in plant DNA histograms, with 2C values for 70 species.
    Biol Cell. 1993;78(1-2):41-51 PMID: 8220226
  39. The Oryza bacterial artificial chromosome library resource: construction and analysis of 12 deep-coverage large-insert BAC libraries that represent the 10 genome types of the genus Oryza.
    Genome Res. 2006 Jan;16(1):140-7 PMID: 16344555
  40. LRR-containing receptors regulating plant development and defense.
    Development. 2004 Jan;131(2):251-61 PMID: 14701679
  41. Palaeogenomics of plants: synteny-based modelling of extinct ancestors.
    Trends Plant Sci. 2010 Sep;15(9):479-87 PMID: 20638891
  42. Synteny and collinearity in plant genomes.
    Science. 2008 Apr 25;320(5875):486-8 PMID: 18436778
  43. The map-based sequence of the rice genome.
    Nature. 2005 Aug 11;436(7052):793-800 PMID: 16100779
  44. A new cacao linkage map based on codominant markers: development and integration of 201 new microsatellite markers.
    Theor Appl Genet. 2004 Apr;108(6):1151-61 PMID: 14760486
Article Info
Journal
Nature genetics
Abbr.
Nat Genet
ISSN
1546-1718
DOI
10.1038/ng.736
Email
xavier.argout@cirad.fr
Published
2011-02-00
Epub
2010-00-26
Pages
101-8
Language
English
Region
United States
NLM ID
9216904
Subset
IM
Corrections
CommentIn
PMID: 21270832
External Links
PubMed source DOI: 10.1038/ng.736 View journal details
Analysis Services
Analysis Services

Contact

No. 2 Wenbo Road, Zhangqiu District, Jinan, Shandong

Qilu Normal University · Genelibs Bioinformatics Lab

750 Shunhua Rd, Jinan

2F, Bldg F, University Science Park

Tel: 0531-88819269

WeChat Official Account

Follow our WeChat subscription account for real-time updates and the latest in medical and biological research.


Business Email

E-mail: product@genelibs.com

Copyright © 2026.Genelibs Jinan Honghui Biotechnology Co., Ltd. 鲁ICP备20007159号-2