Progress report on the sequencing and assembly of the allotetraploid Coffea arabica var. Bourbon genome

It is well known that Coffea arabica is the result of a cross pollination between two Coffea species, very likely Coffea canephora and Coffea eugenioides.  Moreover, arabica can set flowers and fruits by self-fertilization and indeed beans can be obtained by a single and isolated plant. Such reproductive behaviour should find some justification in its genome. A genome sequencing project has been initiated to investigate the structure of the allotetraploid genome of Arabica.

High molecular weight genomic DNA was obtained from entire plantlets of Coffea arabica var. Bourbon and a BAC library was constructed. 175,872 BAC clones were pooled into 96 pools of 384 clones each and the pools underwent DNA sequencing on next generation sequencing Illumina platform. Whole genome shotgun sequencing was also performed on two Illumina libraries with 500 and 800 bp insert size and on one mate-pair library with inserts of 2 Kbp. We additionally performed the sequencing of cDNA libraries (RNA-seq on Illumina platform) obtained from leaves, root and cherries in order to aid gene prediction. A preliminary assembly of the genome has been carried out.  The assembly is now mapped on the available Coffea canephora genome to obtain pseudomolecules.

The preliminary bioinformatics analysis of the arabica genome suggests a high degree of polymorphism between its sub-genomes, in line with the allotetraploid constitution of the Coffea arabica genome.