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Chromosomal-scale and haplotype-resolved genome assembly of the first Trinitario hybrid cacao ICS 1
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  • Published: 19 March 2026

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

  • Xuehuan Feng  ORCID: orcid.org/0000-0002-0732-93221,2,
  • Revanth Sai Kumar Reddy Patel1,
  • Yuchen Yan1,
  • Vaishnavi Annabhemoju1,
  • Lyndel W Meinhardt3,
  • Bryan Bailey3,
  • Sunchung Park  ORCID: orcid.org/0000-0002-7398-94763,
  • Stephen P. Cohen  ORCID: orcid.org/0000-0002-0748-04013,
  • Dapeng Zhang3 &
  • …
  • Yanbin Yin  ORCID: orcid.org/0000-0001-7667-881X1 

Scientific Data , Article number:  (2026) Cite this article

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We are providing an unedited version of this manuscript to give early access to its findings. Before final publication, the manuscript will undergo further editing. Please note there may be errors present which affect the content, and all legal disclaimers apply.

Subjects

  • Genomics
  • Plant sciences

Abstract

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.

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Data availability

All genome sequencing data are available in NCBI through the Umbrella BioProject PRJNA1136499. The gene annotations (protein sequence and GFF files) are available via Figshare65.

Code availability

No original code was developed; all computational analyses were performed with published computer tools.

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Acknowledgements

We thank Indrani K. Baruah for sample preparation, Osman Gutierrez for comments and discussions during the project. This work was primarily funded by the United States Department of Agriculture (USDA)/Agricultural Research Service (ARS) awards [58-8042-9-089, 58-8042-3-076], and partially by the National Institutes of Health (NIH) R01 award [R01GM140370]. X.F. was also supported by a Shandong Agricultural University startup grant (539-700028) after 1/2025. The mention of trade names or commercial products in this publication is for informational purposes only and does not imply endorsement or recommendation by the U.S. Department of Agriculture. The USDA is an equal opportunity provider and employer.

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Authors and Affiliations

  1. Department of Food Science and Technology, Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA

    Xuehuan Feng, Revanth Sai Kumar Reddy Patel, Yuchen Yan, Vaishnavi Annabhemoju & Yanbin Yin

  2. State Key Laboratory of Wheat Improvement, College of Agronomy, Shandong Agricultural University, Tai’an, Shandong, 271018, P. R. China

    Xuehuan Feng

  3. U.S. Department of Agriculture, Sustainable Perennial Crops Laboratory, Beltsville, MD, USA

    Lyndel W Meinhardt, Bryan Bailey, Sunchung Park, Stephen P. Cohen & Dapeng Zhang

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Contributions

Y.Y., D.Z., L.W.M. conceived and designed the project. D.Z., B.B., S.P., S.P.C., L.W.M. collected the Cacao materials and generated the sequencing data. X.F., Y.Yan, R.S.K.R.P performed genome assembly evaluation, annotation, and all data analysis, V.A. contributed to the data analysis and management. X.F., D.Z., Y.Y. draft the manuscript. All authors contributed and approved the final manuscript.

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Feng, X., Patel, R.S.K.R., Yan, Y. et al. Chromosomal-scale and haplotype-resolved genome assembly of the first Trinitario hybrid cacao ICS 1. Sci Data (2026). https://doi.org/10.1038/s41597-026-07054-0

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  • Received: 02 July 2025

  • Accepted: 06 March 2026

  • Published: 19 March 2026

  • DOI: https://doi.org/10.1038/s41597-026-07054-0

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