Chromosome-level genome and annotation data for parentally phased diploid Theobroma cacao clone 26

The genome and annotation data herein relates to the following publication. Please cite the current version of this manuscript if this data is useful to your work https://acsess.onlinelibrary.wiley.com/doi/10.1002/tpg2.20524

Parental assigned chromosomes for cultivated cacao provides insights into genetic architecture underlying resistance to vascular streak dieback

Diseases of Theobroma cacao disrupt cocoa bean supply and economically impact growers. Vascular streak dieback (VSD), caused by Ceratobasidium theobromae, is a new encounter disease of cacao currently contained to southeast Asia and Melanesia. Resistance to VSD has been tested with large progeny trials in Sulawesi, Indonesia, and in Papua New Guinea with the identification of informative quantitative trait loci (QTL). Using a VSD susceptible progeny tree (clone 26), derived from a resistant and susceptible parental cross, we assembled the genome to chromosome-level and discriminated alleles inherited from either resistant or susceptible parents. The parentally phased genomes were annotated for all predicted genes and then specifically for resistance genes of the nucleotide-binding site leucine-rich repeat class (NLR). On investigation, we determined the presence of NLR clusters and other potential disease response gene candidates at informative QTLs. We identified structural variants within NLRs inherited from parentals. Our research provides the first diploid, fully scaffolded and parentally phased genome resource for Theobroma cacao L. and provides insights into the genetics underlying resistance and susceptibility to VSD.