Subject	Biodiversity
Specific subject area	Genomics
Type of data	Genome sequences and table
How the data were acquired	High-throughput DNA sequencing using NovaSeq 6000 and PromethION platforms
Data format	Raw and assembled genome sequences
Description of data collection	The sample was obtained from the muscle tissue of Rhinoceros unicornis at Yokohama Municipal Kanazawa Zoo, Yokohama, Japan (NIES ID: 5488M, female). Genomic DNA was extracted using proteinase K and phenol/chloroform/isoamyl alcohol for short-read sequencing and a NucleoBond HMW DNA extraction kit (Macherey-Nagel, Düren, Germany) for long-read sequencing. Short-read libraries were prepared using a TruSeq LT PCR-free DNA Library Preparation Kit, and sequencing was performed using the NovaSeq 6000 sequencing system (Illumina, San Diego, CA, USA) with 2 × 150 bp paired-end reads. Long-read libraries were prepared using a Ligation Sequencing Kit, and sequencing was performed using the PromethION system (Oxford Nanopore Technologies, Oxford, UK). The short and long reads were assembled into contigs using the HASLR program, which utilizes a hybrid assembly approach.
Data source location	Tsukuba, Ibaraki, Japan
Data accessibility	Data have been deposited in relevant databases and are publicly available. The sequencing data were deposited in the Sequence Read Archive under accession numbers DRR308100 (https://www.ncbi.nlm.nih.gov/sra/?term=DRR308100) and DRR311486 (https://www.ncbi.nlm.nih.gov/sra/?term=DRR311486). The whole-genome sequence, Rhinoceros unicornis ID: 5488M, was deposited in GenBank under accession number BOSQ00000000 (https://www.ncbi.nlm.nih.gov/nuccore/2085786713). All details regarding genome sequencing data are available at NCBI under BioProject accession number PRJDB11285 (https://www.ncbi.nlm.nih.gov/bioproject/PRJDB11285).