Evidence map›Paper›PMID 41857065›Full record

ArticleScientific data2026

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

Xuehuan Feng, Revanth Sai Kumar Reddy Patel, Yuchen Yan, Vaishnavi Annabhemoju, Lyndel W Meinhardt, Bryan Bailey, Sunchung Park, Stephen P Cohen, Dapeng Zhang, Yanbin Yin

Abstract readDataset
PubMed Full text at PMC Publisher
In one paragraph

Article in Scientific data, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

10 authors.

Xuehuan FengDepartment of Food Science and Technology, Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA.ORCID http://orcid.org/0000-0002-0732-9322
Revanth Sai Kumar Reddy PatelDepartment of Food Science and Technology, Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA.
Yuchen YanDepartment of Food Science and Technology, Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA.
Vaishnavi AnnabhemojuDepartment of Food Science and Technology, Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA.
Lyndel W MeinhardtU.S. Department of Agriculture, Sustainable Perennial Crops Laboratory, Beltsville, MD, USA.
Bryan BaileyU.S. Department of Agriculture, Sustainable Perennial Crops Laboratory, Beltsville, MD, USA.
Sunchung ParkU.S. Department of Agriculture, Sustainable Perennial Crops Laboratory, Beltsville, MD, USA.ORCID http://orcid.org/0000-0002-7398-9476
Stephen P CohenU.S. Department of Agriculture, Sustainable Perennial Crops Laboratory, Beltsville, MD, USA.ORCID http://orcid.org/0000-0002-0748-0401
Dapeng ZhangU.S. Department of Agriculture, Sustainable Perennial Crops Laboratory, Beltsville, MD, USA. dapeng.zhang@usda.gov.
Yanbin YinDepartment of Food Science and Technology, Nebraska Food for Health Center, University of Nebraska-Lincoln, Lincoln, NE, USA. yyin@unl.edu.ORCID http://orcid.org/0000-0001-7667-881X

Funding

Exploration of cloud computing for CAZyme researchR01GM140370 · NIGMS · UNIVERSITY OF NEBRASKA LINCOLN · PI YIN, YANBIN · 2021 to 2024
$1.5M
United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service) 58-8042-3-076U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) R01GM140370
6 · The paper itself

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.

Indexed as

CacaoGenome, PlantHaplotypesChromosomes, PlantHaploidy

Identifiers

PMID41857065
PMCPMC13153264

What OpenQuestion holds

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LicenceCC BY-NC-ND
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Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.