ArticleBMC genomics2017
The cacao Criollo genome v2.0: an improved version of the genome for genetic and functional genomic studies.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers, 1 of them a synthesis that pooled it.
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Who cites it
48 citing papers in PubMed, 1 synthesis or guideline pooled it.
- State of the Art of the Molecular Biology of the Interaction between Cocoa and Witches' Broom Disease: A Systematic Review.International journal of molecular sciences · 2023Pooled it
- Association mapping and genome prediction reveal a complex genetic architecture for resistance to black and frosty pod rot in cacao (Theobroma cacao L.) populations.The plant genome · 2026Article
- Genomic Sampling and Population Structure of Farmer-Maintained Varieties Reveal Previously Uncharacterized Diversity of Theobroma cacao L. in Costa Rica.Molecular ecology · 2026Article
- Chromosomal-scale and haplotype-resolved genome assembly of the first Trinitario hybrid cacao ICS 1.Scientific data · 2026Article
- Integrative chromosome-scale genome analysis of cupuassu provides insights into witches' broom disease resistance and expands genomic resources for Theobroma.The plant genome · 2026Article
- Intraspecies sequence-graph analysis of the Phytophthora theobromicola genome reveals a dynamic structure and variable effector repertoires.G3 (Bethesda, Md.) · 2026Article
- Cacao in the Mississippian World: Archaeogenomic evidence for T. cacao consumption at the Etowah Site, Georgia.PloS one · 2026Article
- All roads lead to Rome: integrated physiological and transcriptomic analysis of cacao drought response reveals different ways to achieve tolerance in two hybrid clones.Frontiers in plant science · 2026Article
- Near T2T haplotype-resolved genomes of cacao (Theobroma cacao) variety CCN51.Scientific data · 2025Article
- Developing a core collection for the conservation of Theobroma cacao's genetic diversity.BMC genomics · 2025Article
- Local gene duplications drive extensive NLR copy number variation across multiple genotypes of Theobroma cacao.G3 (Bethesda, Md.) · 2025Article
- A defined microbial community reproduces attributes of fine flavour chocolate fermentation.Nature microbiology · 2025Article
- Machine learning-driven GWAS uncovers novel candidate genes for resistance to frosty pod rot and witches' broom disease in cacao.The plant genome · 2025Article
- Chromosome-level genome assembly of the ornamental plant Alcea rosea.Scientific data · 2025Article
- Wild or Introduced? Investigating the Genetic Landscape of Cacao Populations in South America.Ecology and evolution · 2025Article
- Chromosome-scale genome assembly of Phyllanthus emblica L. 'Yingyu'.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Phylogeny-based comparative analysis of gene expression modulation upon drought stress across three cotton diploids.BMC plant biology · 2025Article
- Article
- Parental assigned chromosomes for cultivated cacao provides insights into genetic architecture underlying resistance to vascular streak dieback.The plant genome · 2024Article
- The cacao gene atlas: a transcriptome developmental atlas reveals highly tissue-specific and dynamically-regulated gene networks in Theobroma cacao L.BMC plant biology · 2024Article
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8 authors.
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Abstract
backgroundTheobroma cacao L., native to the Amazonian basin of South America, is an economically important fruit tree crop for tropical countries as a source of chocolate. The first draft genome of the species, from a Criollo cultivar, was published in 2011. Although a useful resource, some improvements are possible, including identifying misassemblies, reducing the number of scaffolds and gaps, and anchoring un-anchored sequences to the 10 chromosomes.
methodsWe used a NGS-based approach to significantly improve the assembly of the Belizian Criollo B97-61/B2 genome. We combined four Illumina large insert size mate paired libraries with 52x of Pacific Biosciences long reads to correct misassembled regions and reduced the number of scaffolds. We then used genotyping by sequencing (GBS) methods to increase the proportion of the assembly anchored to chromosomes.
resultsThe scaffold number decreased from 4,792 in assembly V1 to 554 in V2 while the scaffold N50 size has increased from 0.47 Mb in V1 to 6.5 Mb in V2. A total of 96.7% of the assembly was anchored to the 10 chromosomes compared to 66.8% in the previous version. Unknown sites (Ns) were reduced from 10.8% to 5.7%. In addition, we updated the functional annotations and performed a new RefSeq structural annotation based on RNAseq evidence.
conclusionTheobroma cacao Criollo genome version 2 will be a valuable resource for the investigation of complex traits at the genomic level and for future comparative genomics and genetics studies in cacao tree. New functional tools and annotations are available on the Cocoa Genome Hub ( http://cocoa-genome-hub.southgreen.fr ).
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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.