Chromosomal-scale and haplotype-resolved genome assembly of the first Trinitario hybrid cacao ICS 1

Cacao (Theobroma cacao L.) is a diploid tropical tree of major economic importance and the source of cocoa beans for the global chocolate industry. Although cacao was traditionally classified into the Criollo, Forastero, and Trinitario groups, genomic studies have revealed extensive genetic diversity shaped by long-term evolution, domestication, and hybridization. Trinitario cacao is a key contributor to fine-flavor cocoa production, valued for its complex sensory attributes but often constrained by lower productivity and stress susceptibility. The Trinitario clone ICS 1 has played a pivotal role in global cacao breeding, serving as a parental line in numerous hybrid combinations due to its favorable flavor quality and self-compatibility. Despite the availability of high-quality reference genomes from several cacao genetic groups, a haplotype-resolved reference genome for Trinitario cacao has been lacking. Here, we present a chromosome-scale, haplotype-resolved genome assembly of ICS 1, providing detailed insights into allelic variation and genome structure. This resource advances cacao breeding, genomic selection, and evolutionary studies, particularly those focused on fine-flavor traits and hybrid genome architecture.