Genome Size Evolution in Theobroma cacao: Recent Sequencing of Two Cacao Genomes of Different Size

Cacao (Theobroma cacao L.) is a tropical understory tree whose seeds are the source of cocoa butter and cocoa for chocolate production.  Two complete cacao genome de novo assemblies have been accomplished from two cacao cultivars ('Matina 1-6' and 'Criollo B1-97/B2') with genomes differing in size by approximately 9%. Different scales of amplification of transposable elements, particularly LTR-retrotransposons are largely responsible for the observed genome size difference. The genome size of genetic subpopulations of Theobroma cacao as well as individuals of other Theobroma species and a related genus, Herrania, have been estimated by flow cytometry and correlated to phylogeny and geographic origin.  Probes made from centromeric repeats have been used with BAC probes to identify each of the 10 chromosomes of cacao and associate them with linkage groups from the genetic recombination map.  The two cacao genomes will be compared in detail with regard to gene content, types, number and positions of transposable elements, and synteny.