title: The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color.
abstract: BACKGROUND
  Theobroma cacao L. cultivar Matina 1-6 belongs to the most cultivated cacao type. The availability of its genome sequence and methods for identifying genes responsible for important cacao traits will aid cacao researchers and breeders.
  
  
  RESULTS
  We describe the sequencing and assembly of the genome of Theobroma cacao L. cultivar Matina 1-6. The genome of the Matina 1-6 cultivar is 445 Mbp, which is significantly larger than a sequenced Criollo cultivar, and more typical of other cultivars. The chromosome-scale assembly, version 1.1, contains 711 scaffolds covering 346.0 Mbp, with a contig N50 of 84.4 kbp, a scaffold N50 of 34.4 Mbp, and an evidence-based gene set of 29,408 loci. Version 1.1 has 10x the scaffold N50 and 4x the contig N50 as Criollo, and includes 111 Mb more anchored sequence. The version 1.1 assembly has 4.4% gap sequence, while Criollo has 10.9%. Through a combination of haplotype, association mapping and gene expression analyses, we leverage this robust reference genome to identify a promising candidate gene responsible for pod color variation. We demonstrate that green/red pod color in cacao is likely regulated by the R2R3 MYB transcription factor TcMYB113, homologs of which determine pigmentation in Rosaceae, Solanaceae, and Brassicaceae. One SNP within the target site for a highly conserved trans-acting siRNA in dicots, found within TcMYB113, seems to affect transcript levels of this gene and therefore pod color variation.
  
  
  CONCLUSIONS
  We report a high-quality sequence and annotation of Theobroma cacao L. and demonstrate its utility in identifying candidate genes regulating traits.
authors.forename: Juan C
authors.initials: JC
authors.lastname: Motamayor
authors.forename: Keithanne
authors.initials: K
authors.lastname: Mockaitis
authors.forename: Jeremy
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authors.lastname: Schmutz
authors.forename: Niina
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authors.lastname: Haiminen
authors.forename: Donald
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authors.lastname: Livingstone
authors.forename: Omar
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authors.lastname: Cornejo
authors.forename: Seth D
authors.initials: SD
authors.lastname: Findley
authors.forename: Ping
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authors.lastname: Zheng
authors.forename: Filippo
authors.initials: F
authors.lastname: Utro
authors.forename: Stefan
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authors.lastname: Royaert
authors.forename: Christopher
authors.initials: C
authors.lastname: Saski
authors.forename: Jerry
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authors.lastname: Jenkins
authors.forename: Ram
authors.initials: R
authors.lastname: Podicheti
authors.forename: Meixia
authors.initials: M
authors.lastname: Zhao
authors.forename: Brian E
authors.initials: BE
authors.lastname: Scheffler
authors.forename: Joseph C
authors.initials: JC
authors.lastname: Stack
authors.forename: Frank A
authors.initials: FA
authors.lastname: Feltus
authors.forename: Guiliana M
authors.initials: GM
authors.lastname: Mustiga
authors.forename: Freddy
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authors.lastname: Amores
authors.forename: Wilbert
authors.initials: W
authors.lastname: Phillips
authors.forename: Jean Philippe
authors.initials: JP
authors.lastname: Marelli
authors.forename: Gregory D
authors.initials: GD
authors.lastname: May
authors.forename: Howard
authors.initials: H
authors.lastname: Shapiro
authors.forename: Jianxin
authors.initials: J
authors.lastname: Ma
authors.forename: Carlos D
authors.initials: CD
authors.lastname: Bustamante
authors.forename: Raymond J
authors.initials: RJ
authors.lastname: Schnell
authors.forename: Dorrie
authors.initials: D
authors.lastname: Main
authors.forename: Don
authors.initials: D
authors.lastname: Gilbert
authors.forename: Laxmi
authors.initials: L
authors.lastname: Parida
authors.forename: David N
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authors.lastname: Kuhn
mesh_terms: D002099:Cacao / Q000235:genetics / Q000378:metabolism; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D003116:Color; D005638:Fruit / Q000235:genetics* / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D059646:Genome Size; D018745:Genome, Plant; D059014:High-Throughput Nucleotide Sequencing; D040641:Quantitative Trait Loci; D019655:Quantitative Trait, Heritable; D034741:RNA, Small Interfering / Q000235:genetics / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D034741:RNA, Small Interfering; D014157:Transcription Factors