title: The genome of Theobroma cacao.
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.
authors.affiliation: 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
authors.forename: Xavier
authors.initials: X
authors.lastname: Argout
authors.forename: Jerome
authors.initials: J
authors.lastname: Salse
authors.forename: Jean-Marc
authors.initials: JM
authors.lastname: Aury
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Guiltinan
authors.forename: Gaetan
authors.initials: G
authors.lastname: Droc
authors.forename: Jerome
authors.initials: J
authors.lastname: Gouzy
authors.forename: Mathilde
authors.initials: M
authors.lastname: Allegre
authors.forename: Cristian
authors.initials: C
authors.lastname: Chaparro
authors.forename: Thierry
authors.initials: T
authors.lastname: Legavre
authors.forename: Siela N
authors.initials: SN
authors.lastname: Maximova
authors.forename: Michael
authors.initials: M
authors.lastname: Abrouk
authors.forename: Florent
authors.initials: F
authors.lastname: Murat
authors.forename: Olivier
authors.initials: O
authors.lastname: Fouet
authors.forename: Julie
authors.initials: J
authors.lastname: Poulain
authors.forename: Manuel
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authors.lastname: Ruiz
authors.forename: Yolande
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authors.lastname: Roguet
authors.forename: Maguy
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authors.lastname: Rodier-Goud
authors.forename: Jose Fernandes
authors.initials: JF
authors.lastname: Barbosa-Neto
authors.forename: Francois
authors.initials: F
authors.lastname: Sabot
authors.forename: Dave
authors.initials: D
authors.lastname: Kudrna
authors.forename: Jetty Siva S
authors.initials: JS
authors.lastname: Ammiraju
authors.forename: Stephan C
authors.initials: SC
authors.lastname: Schuster
authors.forename: John E
authors.initials: JE
authors.lastname: Carlson
authors.forename: Erika
authors.initials: E
authors.lastname: Sallet
authors.forename: Thomas
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authors.lastname: Schiex
authors.forename: Anne
authors.initials: A
authors.lastname: Dievart
authors.forename: Melissa
authors.initials: M
authors.lastname: Kramer
authors.forename: Laura
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authors.lastname: Gelley
authors.forename: Zi
authors.initials: Z
authors.lastname: Shi
authors.forename: Aurélie
authors.initials: A
authors.lastname: Bérard
authors.forename: Christopher
authors.initials: C
authors.lastname: Viot
authors.forename: Michel
authors.initials: M
authors.lastname: Boccara
authors.forename: Ange Marie
authors.initials: AM
authors.lastname: Risterucci
authors.forename: Valentin
authors.initials: V
authors.lastname: Guignon
authors.forename: Xavier
authors.initials: X
authors.lastname: Sabau
authors.forename: Michael J
authors.initials: MJ
authors.lastname: Axtell
authors.forename: Zhaorong
authors.initials: Z
authors.lastname: Ma
authors.forename: Yufan
authors.initials: Y
authors.lastname: Zhang
authors.forename: Spencer
authors.initials: S
authors.lastname: Brown
authors.forename: Mickael
authors.initials: M
authors.lastname: Bourge
authors.forename: Wolfgang
authors.initials: W
authors.lastname: Golser
authors.forename: Xiang
authors.initials: X
authors.lastname: Song
authors.forename: Didier
authors.initials: D
authors.lastname: Clement
authors.forename: Ronan
authors.initials: R
authors.lastname: Rivallan
authors.forename: Mathias
authors.initials: M
authors.lastname: Tahi
authors.forename: Joseph Moroh
authors.initials: JM
authors.lastname: Akaza
authors.forename: Bertrand
authors.initials: B
authors.lastname: Pitollat
authors.forename: Karina
authors.initials: K
authors.lastname: Gramacho
authors.forename: Angélique
authors.initials: A
authors.lastname: D'Hont
authors.forename: Dominique
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authors.lastname: Brunel
authors.forename: Diogenes
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authors.lastname: Infante
authors.forename: Ismael
authors.initials: I
authors.lastname: Kebe
authors.forename: Pierre
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authors.lastname: Costet
authors.forename: Rod
authors.initials: R
authors.lastname: Wing
authors.forename: W Richard
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authors.lastname: McCombie
authors.forename: Emmanuel
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authors.lastname: Guiderdoni
authors.forename: Francis
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authors.lastname: Quetier
authors.forename: Olivier
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authors.lastname: Panaud
authors.forename: Patrick
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authors.lastname: Wincker
authors.forename: Stephanie
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authors.lastname: Bocs
authors.forename: Claire
authors.initials: C
authors.lastname: Lanaud
mesh_terms: D002099:Cacao / Q000235:genetics*; D002467:Cell Nucleus / Q000235:genetics; D004247:DNA / Q000235:genetics; D004251:DNA Transposable Elements; D019143:Evolution, Molecular; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D018745:Genome, Plant; D005838:Genotype; D006720:Homozygote; D017403:In Situ Hybridization; D008957:Models, Genetic; D040641:Quantitative Trait Loci
chemical_list: D004251:DNA Transposable Elements; D004247:DNA