BAC-end sequences analysis provides first insights into coffee (Coffea canephora P.) genome composition and evolution

Dereeper Alexis, Guyot Romain, Tranchant-Dubreuil Christine, Anthony François, Argout Xavier, De Bellis Fabien, Combes Marie-Christine, Gavory Fréderick, De Kochko Alexandre, Kudrna Dave, Leroy Thierry, Poulain Julie, Rondeau Myriam, Song Xiang, Wing Rod A., Lashermes Philippe. 2013. BAC-end sequences analysis provides first insights into coffee (Coffea canephora P.) genome composition and evolution. Plant Molecular Biology, 83 (3) : pp. 177-189.

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Quartile : Q1, Sujet : PLANT SCIENCES / Quartile : Q2, Sujet : BIOCHEMISTRY & MOLECULAR BIOLOGY

Abstract : Coffee is one of the world's most important agricultural commodities. Coffee belongs to the Rubiaceae family in the euasterid I clade of dicotyledonous plants, to which the Solanaceae family also belongs. Two bacterial artificial chromosome (BAC) libraries of a homozygous doubled haploid plant of Coffea canephora were constructed using two enzymes, HindIII and BstYI. A total of 134,827 high quality BAC-end sequences (BESs) were generated from the 73,728 clones of the two libraries, and 131,412 BESs were conserved for further analysis after elimination of chloroplast and mitochondrial sequences. This corresponded to almost 13 % of the estimated size of the C. canephora genome. 6.7 % of BESs contained simple sequence repeats, the most abundant (47.8 %) being mononucleotide motifs. These sequences allow the development of numerous useful marker sites. Potential transposable elements (TEs) represented 11.9 % of the full length BESs. A difference was observed between the BstYI and HindIII libraries (14.9 vs. 8.8 %). Analysis of BESs against known coding sequences of TEs indicated that 11.9 % of the genome corresponded to known repeat sequences, like for other flowering plants. The number of genes in the coffee genome was estimated at 41,973 which is probably overestimated. Comparative genome mapping revealed that microsynteny was higher between coffee and grapevine than between coffee and tomato or Arabidopsis. BESs constitute valuable resources for the first genome wide survey of coffee and provide new insights into the composition and evolution of the coffee genome. (Résumé d'auteur)

Mots-clés Agrovoc : Coffea canephora, Génie génétique, Banque de gènes, Séquence nucléotidique, Chromosome, Transformation génétique, Marqueur génétique, Microsatellite, Carte génétique, Génome

Mots-clés complémentaires : Chromosome artificiel, Bac

Classification Agris : F30 - Plant genetics and breeding

Champ stratégique Cirad : Axe 1 (2005-2013) - Intensification écologique

Auteurs et affiliations

  • Dereeper Alexis, IRD (FRA)
  • Guyot Romain, IRD (FRA)
  • Tranchant-Dubreuil Christine, IRD (FRA)
  • Anthony François, IRD (FRA)
  • Argout Xavier, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0002-0100-5511
  • De Bellis Fabien, CIRAD-BIOS-UMR AGAP (FRA) ORCID: 0000-0001-7070-7691
  • Combes Marie-Christine, IRD (FRA)
  • Gavory Fréderick, Centre national de séquençage (FRA)
  • De Kochko Alexandre, IRD (FRA)
  • Kudrna Dave, University of Arizona (USA)
  • Leroy Thierry, CIRAD-BIOS-UMR AGAP (FRA)
  • Poulain Julie, Institut de génomique (FRA)
  • Rondeau Myriam, IRD (FRA)
  • Song Xiang, University of Arizona (USA)
  • Wing Rod A., University of Arizona (USA)
  • Lashermes Philippe, IRD (FRA)

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