Three Near telomere-to-telomere Genomes for Gardenia jasminoides

Gardenia jasminoides, an evergreen shrub in the Rubiaceae family, is widely cultivated across southern China, particularly in regions south of the Yangtze River. With a long history of use in traditional Chinese medicine, its fruits and flowers are valued for their rich diversity of bioactive compounds. In this study, Oxford Nanopore (ONT) sequencing produced 37-34 Gb of long-read data (60-66× coverage) per accession. Complementary PacBio HiFi sequencing generated 28-32 Gb (50-58× coverage), while Hi-C sequencing provided 61-67 Gb (108-119× coverage) to support chromosome-scale assembly. To ensure accuracy, contigs were polished through multiple iterations using Medaka (ONT-based) and Racon (HiFi-based). The final assemblies resolved all 11 chromosomes at telomere-to-telomere continuity, with no gaps. Functional annotation assigned roles to more than 94% of predicted genes (34,397-34,440) through homology and domain-based searches. This high-quality genome resource enables the study of structural variation underlying agronomic traits and supports advances in molecular breeding, bioactive compound biosynthesis, and comparative genomics in Gardenia.