De novo sequencing, assembly, and annotation of the coffee genome using next generation sequencing platforms. We will target the two cultivated Coffea species, C. arabica and C. canephora, to facilitate future marker assisted breeding and positional cloning of agronomically important genes, comparative analysis of gene structure and function, as well as diversity studies. The construction of integrated genetic and physical maps will facilitate genome assembly and comparative studies of gene rearrangements with other Coffea species (>100 diploid species). Our strategy includes:
- Construction of BAC libraries for the allotetraploid c. arabica and its two diploid parental species c. canephora and c. eugenioides.
- Physical map construction based on a combination of BAC end-sequencing and/or BAC fingerprinting, and high density of anchor markers (SSRs and SNPs) covering the complete genome.
- De novo deep coverage sequencing of the coffee genome using next generation sequencing platforms. The availability of deep coverage reference genomes for the diploid species C. canephora and C. eugenioides will serve as robust framework for the sequencing and assembly of the genome of the allotetraploid species C. arabica.
Why to sequence the coffee genome ? read the concept note