Dihaploid Coffea arabica genome sequencing and assembly [W180]

De Kochko Alexandre, Crouzillat Dominique, Rigoreau Michel, Lepelley Maud, Bellanger Laurence, Merot l'Anthoene Virginie, Vandecasteele Céline, Guyot Romain, Poncet Valérie, Tranchant-Dubreuil Christine, Hamon Perla, Hamon Serge, Couturon Emmanuel, Descombes Patrick, Moine Deborah, Mueller Lukas, Strickler Susan R., Andrade Alan A., Protasio Pereira Luiz Filipe, Marraccini Pierre, Giuliano Giovanni, Fiore Alessia, Pietrella Marco, Aprea Giuseppe, Ming Ray, Wai Jennifer, Domingues Douglas S., Paschoal Alexandre, Kuhn Gerrit, Korlach Jonas, Chin Jason, Sankoff David, Zheng Chunfang, Albert Victor A.. 2015. Dihaploid Coffea arabica genome sequencing and assembly [W180]. In : Plant and Animal Genomes Conference XXIII Conference, San diego, United States, San Diego, United States, January 10-14, 2015. s.l. : s.n., Résumé Plant and Animal Genome Conference. 23, San Diego, États-Unis, 10 January 2015/14 January 2015.

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Abstract : Coffea arabica which accounts for 70% of world coffee production is an allotetraploid with a genome size of approximately 1.3 Gb and is derived from the hybridization of C. canephora (710 Mb) and C. eugenioides (670 Mb). To elucidate the evolutionary history of C. arabica, and generate critical information for breeding programs, a sequencing project is underway to finalize a reference genome using a dihaploid line and a set of 30 C. arabica accessions. For the reference genome, we have generated two assemblies, one from Illumina data (>150x coverage) and a second from PacBio sequences (>50x coverage). The present assemblies cover 1,031 and 1,042 Mb, respectively. After further refinement, using Illumina mate pairs and optical mapping, the genome assemblies will be annotated using RNA-Seq. Resequencing of C. eugenioides and C. canephora has been completed and is being used to better assess homeologs within the sub-genomes. Furthermore, 30 C. arabica accessions, representing wild and cultivated genotypes, are being resequenced (20x coverage) using Illumina. A C. arabica genetic map, currently including over 600 SSR markers, that differentiate between the two sub-genomes, is used to anchor the assemblies. Newly identified SNP markers are being added to the map. The final goals of the project are to produce a high quality reference genome, assess an eventual neo-diversification occurring in the cultivated varieties, have a better understanding of the species formation and evolution, and develop tools that will make the finished genome accessible and useful to breeders and researchers. (Texte intégral)

Classification Agris : F30 - Plant genetics and breeding

Auteurs et affiliations

  • De Kochko Alexandre, IRD (FRA)
  • Crouzillat Dominique, Nestlé (FRA)
  • Rigoreau Michel, Nestlé (FRA)
  • Lepelley Maud, Nestlé (FRA)
  • Bellanger Laurence, Nestlé (FRA)
  • Merot l'Anthoene Virginie, Nestlé (FRA)
  • Vandecasteele Céline, Nestlé (FRA)
  • Guyot Romain, IRD (FRA)
  • Poncet Valérie, IRD (FRA)
  • Tranchant-Dubreuil Christine, IRD (FRA)
  • Hamon Perla, IRD (FRA)
  • Hamon Serge, IRD (FRA)
  • Couturon Emmanuel, IRD (FRA)
  • Descombes Patrick, NIHS (CHE)
  • Moine Deborah, NIHS (CHE)
  • Mueller Lukas, Boyce Thompson Institute for Plant Research (USA)
  • Strickler Susan R., Boyce Thompson Institute for Plant Research (USA)
  • Andrade Alan A., EMBRAPA (BRA)
  • Protasio Pereira Luiz Filipe, EMBRAPA (BRA)
  • Marraccini Pierre, CIRAD-BIOS-UMR AGAP (BRA) ORCID: 0000-0001-7637-6811
  • Giuliano Giovanni, ENEA (ITA)
  • Fiore Alessia, ENEA (ITA)
  • Pietrella Marco, ENEA (ITA)
  • Aprea Giuseppe, ENEA (ITA)
  • Ming Ray, University of Illinois (USA)
  • Wai Jennifer, University of Illinois (USA)
  • Domingues Douglas S., IAPAR (BRA)
  • Paschoal Alexandre, UEL (BRA)
  • Kuhn Gerrit, Pacific Biosciences (USA)
  • Korlach Jonas, Pacific Biosciences (USA)
  • Chin Jason, Pacific Biosciences (USA)
  • Sankoff David, University of Ottawa (CAN)
  • Zheng Chunfang, University of Ottawa (CAN)
  • Albert Victor A., University at Buffalo (USA)

Source : Cirad - Agritrop (

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