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

Alexis Dereeper, Romain Guyot, Christine Tranchant-Dubreuil, François Anthony, Xavier Argout, Fabien de Bellis, Marie Christine Combes, Frederick Gavory, Alexandre de Kochko, Dave Kudrna, Thierry Leroy, Julie Poulain, Myriam Rondeau, Xiang Song, Rod Wing, Philippe Lashermes

Research output: Contribution to journalArticlepeer-review

14 Scopus citations

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.

Original languageEnglish (US)
Pages (from-to)177-189
Number of pages13
JournalPlant Molecular Biology
Volume83
Issue number3
DOIs
StatePublished - Oct 2013

Keywords

  • BAC library
  • Coffea
  • Comparative genomics
  • Genome
  • Microsatellites
  • Transposable elements

ASJC Scopus subject areas

  • Genetics
  • Agronomy and Crop Science
  • Plant Science

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