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Three de novo assembled wild cacao genomes from the Upper Amazon

Authors :
Orestis Nousias
Jinfang Zheng
Tang Li
Lyndel W. Meinhardt
Bryan Bailey
Osman Gutierrez
Indrani K. Baruah
Stephen P. Cohen
Dapeng Zhang
Yanbin Yin
Source :
Scientific Data, Vol 11, Iss 1, Pp 1-9 (2024)
Publication Year :
2024
Publisher :
Nature Portfolio, 2024.

Abstract

Abstract Theobroma cacao, the chocolate tree, is indigenous to the Amazon basin, the greatest biodiversity hotspot on earth. Recent advancement in plant genomics highlights the importance of de novo sequencing of multiple reference genomes to capture the genome diversity present in different cacao populations. In this study, three high-quality chromosome-level genomes of wild cacao were constructed, de novo assembled with HiFi long reads sequencing, and scaffolded using a reference-free strategy. These genomes represent the three most important genetic clusters of cacao trees from the Upper Amazon region. The three wild cacao genomes were compared with two reference genomes of domesticated cacao. The five cacao genetic clusters were inferred to have diverged in the early and middle Pleistocene period, approximately 1.83–0.69 million years ago. The results shown here serve as an example of understanding how the Amazonian biodiversity was developed. The three wild cacao genomes provide valuable resources for studying genetic diversity and advancing genetic improvement of this species.

Subjects

Subjects :
Science

Details

Language :
English
ISSN :
20524463
Volume :
11
Issue :
1
Database :
Directory of Open Access Journals
Journal :
Scientific Data
Publication Type :
Academic Journal
Accession number :
edsdoj.b4e9aec828d4581b046a018b08d8cb0
Document Type :
article
Full Text :
https://doi.org/10.1038/s41597-024-03215-1