If200 Dh If200 Dh

80,813 52,416 55,296

150 kb 121 kb

HindIII HindIII HindIII

~7.9x ~6.9x

Noir et al. (2004) Jones et al. (2006) Leroy et al. (2005) de Kochko A., Lashermes

P. and Wing R. A. de Kochko A., Lashermes P. and Wing R. A.

'Calculated for an average genome size of 1300Mb for C. arabica and 700Mb for C. canephora. D.H., doubled haploid.

'Calculated for an average genome size of 1300Mb for C. arabica and 700Mb for C. canephora. D.H., doubled haploid.

highly similar subgenomes has greatly limited the use of chromosome walking and positional cloning approaches. To overcome this complexity and to access a wider range of genetic diversity, the research and development of resources has also focused on the cultivated ancestral diploid progenitor C. canephora. Different large-insert C. canephora BAC libraries have been produced.

The first C. canephora BAC library was constructed in 2005, using the clone IF126, a hybrid between two distinct genetic groups within C. canephora: Congolese and Guinean (Moschetto et al., 1996). This library contained 55,296 clones (average size of 135 Kb), providing coverage of about 10 genome equivalents (Leroy et al., 2005). Initially, it was used to investigate the genome organization of genes involved in sugar metabolism (Leroy et al., 2005). Later, the characterization of CcEIN4 and CcCCoAOMTgenes encoding an ethylene receptor and a caffeic acid O-methyltransferase, respectively, demonstrated its value in identifying genes of agronomical interest in C. canephora (Bustamante-Porras et al., 2007; Chabrillange et al., 2006; Guyot et al., 2009). The genomic sequence of the C. canephora CcEIN4 region was compared to that of several sequenced dicotyledonous genomes (such as Arabidopsis, Medicago truncatula, tomato and grape) that covered the Euasterid and Eurosid clades. Extensive conservation between C. canephora and most of the genomes studied was demonstrated; locally the gene content and order were shown to be highly conserved. The highest degree of microcollinearity was found between C. canephora and V. vinifera, which belong, respectively, to Euasterids and Eurosids, two clades that diverged more than 114 million years ago (Guyot et al., 2009).

The two other C. canephora BAC libraries were constructed with the genomic DNA of a doubled haploid (DH) line derived from the clone IF200. The BAC libraries were prepared with two restriction enzymes Hin-dIII and BstYI, respectively, and include 36,864 clones each (Table II). The two libraries were completed with a total ~16 genome equivalents, providing the basic resources for an international initiative for the construction of a physical map of C. canephora. Sequencing of the 72,000 BAC ends was recently initiated at Genoscope (France).

Finally, a C. eugenioides (the putative maternal parent of C. arabica) BAC library was recently funded (http://www.fontagro.org/). It will be constructed with the aim of sequencing the BAC ends and constructing a physical map. Altogether these genomic resources will rapidly promote the development of homeologous comparative sequence analysis studies between C. arabica and its diploid progenitors. Comparative sequence mapping could answer several questions concerning C. arabica such as what are the consequences of interspecific hybridization on reshaping the genomes and on genome evolution.

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