Three new Theobroma cacao chromosome level genome assemblies for SCA_6, IMC-67 and POUND 7. Three new Theobroma cacao chromosome level genome assemblies for SCA_6, IMC-67 and POUND 7

Theoborma cacao, the chcolate tree, is indigenous to the Amazon basin, the greatest biodiversity hotspot on earth. Large intra-specific variations have been observed among various cacao populations, yet the mechanisms responsible for the origin of this rich diversity remain unresolved. In this study, we constructed three high-quality chromosome-level genomes de novo assembled using PacBio HiFi long reads and scaffolded using a reference-free strategy. These genomes represent the three most important genetic clusters of wild cacao trees from the Upper Amazon region. The three wild cacao genomes were compared with two reference genomes of domesticated cacao. We found that the five cacao genetic clusters diverged in the early and middle Pleistocene period, approximately 1.83 – 0.69 million years ago. This challenges the exisiting Pleistocene refugia hypothesis that suggests a more recent cacao intra-specific diversification. We also found significantly higher percentages of transpolable elements and lower numbers of resistance genes in wild cacao genomes than domesticated reference genomes. The three wild cacao genomes provide valuable resources for studying the cacao genetic diversity.