Chromosome-level genome assembly of the medicinal plant Ophiorrhiza japonica Blume

Ophiorrhiza japonica, a medicinal plant of Rubiaceae, has been selected as a model plant for the study of MIA biosynthesis and regulation, as well as a sustainable source of camptothecin. Here, we performed an assembly and annotation of O. japonica genome. To achieve this, we employed a range of advanced techniques, including flow cytometry, PacBio HiFi sequencing, ONT RNA-sequencing and Hi-C technology. This approach enabled us to construct a high quality, chromosome-level genome of O. japonica. The assembled O. japonica genome spanned 549.81 Mb with a contig N50 size of 43 Mb and a scaffold N50 size of 46.45 Mb. The 24 contigs, representing 99.42% of the total assembled genome, were anchored to 11 chromosomes using Hi-C scaffolding. A total of 313.49 Mb of repeat sequences were identified and 28,182 protein-coding genes were predicted. The findings of this study provide invaluable genomic resources that will facilitate a deeper understanding of species evolution and enable the investigation of a range of crucial traits.