A near-complete genome assembly of Cinchona calisaya

Rubiaceae plants are globally widespread and possess significant economic and medicinal value. Such as the globally important crop of coffee, and Cinchona calisaya Wedd., which is rich in alkaloids, is an important medicinal resource for treating malaria. In recent years, several genome resources of Rubiaceae have been reported. However, the comprehensive phylogenetic relationships of Rubiaceae are still unknown. In this study, we present a nearly complete diploid genome assembly of C. calisaya, characterized by a genome size of 869.93 Mb, and contig N50 length of 44.34 Mb. Notably, 99.75% of the sequences have been successfully anchored to 17 chromosomes, with only 12 gaps remaining. BUSCO assessment indicates that 97.40% of complete core genes are present in the assembly. We identified a total of 42,741 protein-coding genes, among which 38,022 (89.00%) have received functional annotation. The high continuity and integrity of the C. calisaya genome provide a robust foundation for functional genomics research, varietal improvement, and the conservation of genomic resources in medicinal plants.