For whole-genome assembly, D. kaki cv. Taishu young leaves were sampled at Grape and Persimmon Research Station, the Institute of Fruit Tree and Tea Science, National Agriculture and Food Research Organization (NARO). Genomic DNA for sequencing was extracted using the Qiagen Genome-tip G100. The genome DNA was sheared into ∼20 kb DNA fragments with a g-tube machine (Covaris, Woburn, MA, USA), and a HiFi SMRTbell library was constructed with a SMRTbell Express Template Prep Kit 2.0 (PacBio, Menlo Park, CA, USA). The library DNA was fractionated using the BluePippin (Sage Science, Beverly, MA, USA) to eliminate fragments <20 kb and sequenced with a Four SMRT cell 8M on the Sequel II system (PacBio). The sequence reads were converted into HiFi reads with the CCS pipelines (PacBio, https://ccs.how) and assembled with Hifiasm (Cheng et al. 2021 (link)). The obtained contigs were aligned to a reference genome sequence of diploid D. lotus male cv. Kunsenshi-male (Akagi et al. 2020 ; 2n = 2x = 30, 2A + XY) for scaffolding by using RaGOO/RagTag (Alonge et al. 2019 (link), 2022 (link)) to build pseudomolecule sequences, finally with manual revisions.