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

Authors: FENG, XUEHUAN - University Of Nebraska; PATEL, R.S.K.R. - University Of Nebraska; YAN, Y. - University Of Nebraska; ANNABHEMOJU, VAISHNAVI - University Of Nebraska; Meinhardt, Lyndel; BAILEY, BRYAN - Retired ARS Employee; Park, Sunchung; Cohen, Stephen; Zhang, Dapeng; YIN, YANBIN - University Of Nebraska

Submitted to: Scientific Data
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/6/2026
Publication Date: 3/19/2026
Citation: Feng, X., Annabhemoju, V., Meinhardt, L.W., Bailey, B., Park, S., Cohen, S.P., Zhang, D., Yin, Y. 2026. Chromosomal-scale and haplotype-resolved genome assembly of the first Trinitario cacao “ICS 1”. Scientific Data. 13:713. https://doi.org/10.1038/s41597-026-07054-0.
DOI: https://doi.org/10.1038/s41597-026-07054-0

Interpretive Summary: Cacao is a vital agricultural commodity that yields cocoa butter and powder, both of which are essential to the confectionery industry and the production of chocolate. Globally, approximately 10% of cacao beans are classified as fine flavored cacao and are sold at a premium for high-end chocolate products. The Trinitario cacao varieties are key sources of fine flavor beans, among which the variety ICS 1 stands out due to its high productivity and superior bean quality. ICS 1 is also valuable for breeding, as it passes on quality flavor and high yield traits. In this study, the entire genetic blueprint or genome of ICS 1 was mapped using advanced sequencing methods. A total of 22,370 genes were identified. This new genetic information will help scientists understand what makes Trinitario cacao special, including how it produces better quality beans and high yields. With these insights, cacao breeders can develop stronger, higher-yielding plants that resist environmental stresses and diseases, thus ensuring better cacao for the future.

Technical Abstract: Cocoa is a vital agricultural commodity that yields cocoa butter and powder, both essential to the confectionery industry. Globally, approximately 10% of cacao beans are classified as fine flavor cocoa, sold at a premium for high-end chocolate products. 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 for its excellent combining ability, making it a valuable parent in breeding programs aimed at merging desirable agronomic traits with fine flavor bean quality. In this study, we present high-quality, chromosome-level, haplotype-resolved genome assemblies for the first Trinitario hybrid cacao variety, ICS-1. Using PacBio HiFi and Hi-C sequencing, we generated two haplotype 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, aligning with genome size estimates. Genome annotation identified ~22,370 protein-coding genes, with repetitive content of 62.19% and 65.14%, respectively. BUSCO completeness exceeded 98%, confirming high assembly quality. These novel genomic resources will significantly enhance our understanding of the superior phenotypic traits of Trinitario cacao, including heterosis and bean quality. Insights from this research will empower cacao breeders to develop high-yielding, climate-resilient, fine flavor varieties, addressing challenges such as declining soil fertility, rising disease pressures, and accelerating climate change.