A Near Complete Genome Assembly of the Oshima Cherry Cerasus speciosa
The Oshima cherry (Cerasus speciosa), which is endemic to Japan, has significant cultural and horticultural value. In this study, we present a near complete telomere-to-telomere genome assembly for C. speciosa, derived from the old growth "Sakurakkabu" tree on Izu Oshima Island. Using Illumina short-read, PacBio long-read, and Hi-C sequencing, we constructed a 269.3 Mbp genome assembly with a contig N50 of 32.0 Mbp. We examined the distribution of repetitive sequences in the assembled genome and identified regions that appeared to be centromeric. Detailed structural analysis of these putative centromeric regions revealed that the centromeric regions of C. speciosa comprised repetitive sequences with monomer lengths of 166 or 167 bp. Comparative genomic analysis with Prunus sensu lato genome revealed structural variations and conserved syntenic regions. This high-quality reference genome provides a crucial tool for studying the genetic diversity and evolutionary history of Cerasus species, facilitating advancements in horticultural research and the preservation of this iconic species.
Authors
- Hiroyuki Yano (ORCID: https://orcid.org/0000-0002-4265-1149)
- Momi Tsuruta (ORCID: https://orcid.org/0000-0002-5530-1674)
- Takushi Kishida (ORCID: https://orcid.org/0000-0002-2220-7892)
- Bhim B. Biswa (ORCID: https://orcid.org/0000-0002-5582-3982)
- Chikahiko Suzuki
- Ken–Ichi Nonomura (ORCID: https://orcid.org/0000-0002-2057-543X)
- Atsushi Toyoda (ORCID: https://orcid.org/0000-0002-0728-7548)
- Kazumichi Fujiwara (ORCID: https://orcid.org/0000-0002-7840-4676)
- Shoko Kawamoto (ORCID: https://orcid.org/0000-0002-6404-3443)
- Akatsuki Kimura (ORCID: https://orcid.org/0000-0003-4227-4811)
- Kaoru Umehara (ORCID: https://orcid.org/0000-0002-7017-2698)
- Tsuyoshi Koide (ORCID: https://orcid.org/0000-0002-1055-9073)
- Noriko Kimura (ORCID: https://orcid.org/0000-0001-8160-3687)
- Hironori Niki (ORCID: https://orcid.org/0000-0002-5391-6595)
- Yasukazu Nakamura (ORCID: https://orcid.org/0000-0002-6782-5715)
- Tazro Ohta (ORCID: https://orcid.org/0000-0003-3777-5945)
- Yutaka Sato (ORCID: https://orcid.org/0000-0002-0751-6611)
- Toshio Katsuki
Institutions
- Nihon University (JP)
- National Institute of Genetics (JP)
- Chiba University (JP)
- Gunma Prefectural Women's University (JP)
- The Graduate University for Advanced Studies, SOKENDAI (JP)
- Forestry and Forest Products Research Institute (JP)
Publication Details
- Journal
- Scientific Data
- Published
- 2025-02-04
- DOI
- https://doi.org/10.1038/s41597-025-04388-z
- Citations
- 3
- Primary Topic
- Plant Pathogens and Fungal Diseases
- Type
- article
- Field-Weighted Citation Impact
- 3.45
Funders
- Research Organization of Information and Systems