Coffee genome assembly and transcriptome analysis
PAG-2013 P0802, Coffee Transcriptome analysis using RNA sequencing:
Comparison of coffees grown at different altitudes. Juan F. Medrano (1), Ricardo Koyner (2), Alma Islas-Trejo1 (1), Gonzalo Rincon (1).
(1) University of California, Davis, CA 95619, (2) Kotowa Farms, Boquete, Panama
PAG-2017 W176: Update on sequencing of the Coffea arabica variety, Geisha
Allen Van Deynze, Amanda Hulse-Kemp, Dario Cantu and Juan F. Medrano University of California, Davis, CA, 95616
Sequence assembly Coffee arabica UCDv0.5 can be found in Phytozome
The genome was sequenced using Pacific Biosciences (Menlo Park, CA, USA) SMRT technology totaling 95,155 Million base pairs or an estimated 86 genome equivalents. The primary assembly was conducted using Falcon Unzip by Jason Chin (Pacific Biosciences, Menlo Park, USA). It was assembled into 2,684 scaffolds, of which 683 represented 90% of the genome, totaling 1.19 billion base pairs with aid of Chicago libraries from Dovetail Genomics (Santa Cruz, USA). The genome was annotated with support from more than 13 plant tissues collected at different growth stage of UCG-17 and other accessions with Computomics (Tübingen, Germany). An estimated 70,830 genes were predicted to be in coffee.