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

Cocoa is a vital agricultural commodity that yields cocoa butter and powder, both essential to the confectionery industry. The Trinitario cacao varieties are key sources of fine flavor beans, among which ICS 1 stands out due to its high productivity and superior bean quality. ICS 1 is also recognized as a valuable parent in breeding programs for desirable agronomic traits such as fine flavor bean quality. Using sequencing reads from PacBio HiFi and Hi-C technologies, we generated two haploid genome assemblies (374.4 Mb and 410.8 Mb), characterized by low scaffold numbers, high N50 values (39.5 Mb and 39.7 Mb), and 10 pseudo-chromosomes. Genome annotation identified 22,477 and 22,263 protein-coding genes, with repeat content of 62.19% and 65.14%, respectively. BUSCO completeness exceeded 98%, confirming high assembly quality. Cacao breeders will benefit from these haploid genomes to develop high-yielding, climate-resilient, fine flavor cacao varieties, addressing challenges such as declining soil fertility, rising disease pressures, and accelerating climate change.