Near T2T haplotype-resolved genomes of cacao (Theobroma cacao) variety CCN51

As a cornerstone of the global chocolate industry, cacao cultivation supports millions of livelihoods. The modern hybrid variety CCN51 is the most widely planted cultivar in Latin America, valued for its exceptional yield, broad disease resistance, and superior adaptability. Here, we present a high-quality, haplotype-resolved, near Telomere-to-Telomere (T2T) genome assembly for CCN51, generated using PacBio HiFi long-reads and Hi-C data. The assembly spans 414.0 Mb and 417.7 Mb for the two haplotypes and exhibits a high k-mer completeness of 99.24%. Our comprehensive annotation predicted 22,941 and 22,948 protein-coding genes in the two haplotypes, respectively. Furthermore, our improved analysis of transposable elements (TEs) revealed a high TE content of 62.36% in CCN51, with a classification rate of 59%, representing a significant improvement over previous reports. This comprehensive genomic resource provides a vital foundation for deciphering the genetic basis of CCN51's exceptional agronomic traits. The genomic data generated from this work will directly support genomics-assisted breeding, facilitating the development of high-yield, high-quality cacao varieties with enhanced resilience to environmental and biological stresses.