W189
Building High Quality Reference Genome Assemblies using PACBio long reads for the Allotetraploid Coffea arabica and its Diploid Ancestral Maternal Species Coffea eugenioides

Date: Sunday, January 10, 2016
Time: 4:00 PM
Room: Pacific Salon 3
Marcela Yepes , Cornell University/ School of Integrative Plant Sciences/ Plant Pathology and Plant Microbe Biology Section, Geneva, NY
Alvaro Gaitan , Centro Nacional de Investigaciones de Cafe, CENICAFE, Chinchiná, Colombia
Marco A. Cristancho , Colombian Center for Bioinformatics and Computational Biology (Bios), Manizales, Caldas, Colombia
Luis Fernando Rivera , Colombian Center for Bioinformatics and Computational Biology (Bios), Manizales, Caldas, Colombia
Juan Carlos Correa , Colombian Center for Bioinformatics and Computational Biology (Bios), Manizales, Caldas, Colombia
Carlos Ernesto Maldonado , Centro Nacional de Investigaciones de Cafe, CENICAFE, Chinchiná, Colombia
Carmenza E. Gongora , Centro Nacional de Investigaciones de Cafe, CENICAFE, Chinchiná, Colombia
Andres Mauricio Villegas , Centro Nacional de Investigaciones de Cafe, CENICAFE, Chinchiná, Colombia
Huver Posada , Federacion Nacional de Cafeteros de Colombia (FNC)/ Centro Nacional de Investigaciones de Café (CENICAFE), Chinchina, Caldas, Colombia
Aleksey Zimin , University of Maryland, College Park, MD
James A. Yorke , University of Maryland, College Park, MD
Keithanne Mockaitis , Indiana University, Bloomington, IN
Herb Aldwinckle , Cornell University/ School of Integrative Plant Sciences/ Plant Pathology and Plant Microbe Biology Section, Geneva, NY
Allopolyploids originate from hybridization between divergent genomes associated with chromosome set doubling.  As a consequence, the genomes may undergo a wide range of structural, epigenetic, and functional changes. The world’s most widely cultivated coffee species, representing 70% of the coffee market, is the allotetraploid, Coffea arabica (2n=4x=44; genome size 1.3 Gb).  C. arabica evolved through the interspecific hybridization of the ancestors of two diploid Coffea species:  Coffea eugenioides (2n=22, maternal donor, genome size 0.66 Gb) and C. canephora (2n=22, paternal donor, genome size 0.71 Gb).  Sequencing and assembly of the C. canephora genome was published recently, Denoeud et al. 2014.  Science 345: 1181-1184; genome assembly can be accessed at: http://coffee-genome.org.  We report here progress to produce high quality reference assemblies for C. eugenioides and C. arabica using Pacific BioSciences (PACBio) long reads to enable coffee genetics and genomics of coffee and speed up adaptation of the crop to climate change.  Climate change is probably the most severe threat currently facing the coffee industry on the global scale.  In recent years, extreme weather events in Central America, Colombia, and Brazil have led to coffee production losses of more than US $2 bn.  Of major concern is the very narrow genetic base of cultivated coffee varieties, and therefore the urgent need to develop advanced genomic tools to speed up characterization of Coffea diversity in its Center of Origin, Ethiopia, which accounts for 98% of the genetic pool, to help broaden the genetic base of cultivated C. arabica and speed up adaptation of the crop to climate change.

This abstract will have an extended time and will be presented by co-authors Marcela Yepes and Marco Cristancho.