The Genome of the Tetraploid arabica Coffee and its Diploid Ancestors

Arabica Coffee Genome Consortium (ACGC)

Coffea arabica accounts for 70% of world coffee production and is threatened by various biotic and abiotic factors. It is an allotetraploid (2n=4x=44) with a genome size of approximately 1.3 Gb, derived from the recent (< 0.6 mya) hybridization of two diploid progenitors (2n=2x=22), C. canephora (710 Mb) and C. eugenioides (670 Mb). In an effort to better understand the complex evolutionary history of C. arabica, PacBio sequences were generated for C. arabica, C. canephora, and C. eugenioides at a minimum of 50x coverage for each genome and assembled. Resulting contigs were scaffolded and anchored to pseudomolecules based on genetics maps. Optical maps were used for further scaffolding and improvement of the C. arabica genome. The present assemblies for C.arabica, C. canephora, and C. eugenioides, cover 1.1 Gbp, 669 Mbp, and 660 Mbp of the genome, with contig N50 values of 279 kbp, 973 kbp, and 879 kbp respectively. Approximately 33%, 55%, and 48% of each genome has been anchored to the genetic map. The genome assemblies have been annotated using expression data, including Iso-Seq and RNA-seq, as well as protein data. Comparative genomics, gene family analysis, and other studies are shedding light on important features in these three genomes. In addition, 35 C. arabica varieties (cultivated) and accessions (wild) were also sequenced using Illumina reads for diversity analysis. These high quality reference coffee genomes will provide powerful genomic tools to enable more efficient coffee breeding strategies which will be important for improved resistance to the stressors that pressure Coffea.