Phased genome assemblies and pangenome graphs of human populations of Japan and Saudi Arabia
The selection of a reference sequence in genome analysis is critical, as it serves as the foundation for all downstream analyses. Recently, the pangenome graph has been proposed as a data model that incorporates haplotypes from multiple individuals. Here we present JaSaPaGe, a pangenome graph reference for Saudi Arabian and Japanese populations, both of which have been significantly underrepresented in previous genomic studies. We constructed JaSaPaGe from high-quality phased diploid assemblies which were made utilizing PacBio high-fidelity long reads, Nanopore long reads, and Hi-C short reads of 9 Saudi and 10 Japanese individuals. Quality evaluation of the pangenome graph by variant calling showed that our pangenome outperformed earlier linear reference genomes (GRCh38 and T2T-CHM13) and showed comparable performance to the pangenome graph provided by the Human Pangenome Reference Consortium (HPRC), with more variants found in Japanese and Saudi samples using their population-specific pangenomes. This pangenome reference will serve as a valuable resource for both the research and clinical communities in Japan and Saudi Arabia.
Authors
- Yosuke Kawai (ORCID: https://orcid.org/0000-0003-0666-1224)
- Masao Nagasaki
- Ebtehal Alsolme (ORCID: https://orcid.org/0000-0001-6638-4164)
- Toshiaki Katayama (ORCID: https://orcid.org/0000-0003-2391-0384)
- Saeideh Ashouri (ORCID: https://orcid.org/0000-0002-5021-5144)
- Katsushi Tokunaga (ORCID: https://orcid.org/0000-0001-5501-0503)
- Robert Hoehndorf (ORCID: https://orcid.org/0000-0001-8149-5890)
- Yutaka Suzuki (ORCID: https://orcid.org/0000-0003-4852-1879)
- Yasuyuki Ohkawa (ORCID: https://orcid.org/0000-0001-6440-9954)
- Marwa Abdelhakim (ORCID: https://orcid.org/0000-0001-6816-2119)
- Malak Abedalthagafi (ORCID: https://orcid.org/0000-0003-1786-3366)
- Rund Tawfiq (ORCID: https://orcid.org/0000-0002-7052-573X)
- Maxat Kulmanov (ORCID: https://orcid.org/0000-0003-1710-1820)
- Yang Liu (ORCID: https://orcid.org/0000-0001-5767-360X)
Institutions
- Tufts University (US)
- Tufts Medical Center (US)
- Kyushu University (JP)
- Kyoto University (JP)
- King Fahd Medical City (SA)
- National Center for Global Health and Medicine (JP)
- King Salman Center for Disability Research (SA)
- Research Organization of Information and Systems (JP)
- King Abdullah University of Science and Technology (SA)
- The University of Tokyo (JP)
Publication Details
- Journal
- Scientific Data
- Published
- 2025-08-12
- DOI
- https://doi.org/10.1038/s41597-025-05652-y
- Citations
- 1
- Primary Topic
- Genomics and Rare Diseases
- Type
- article
- Field-Weighted Citation Impact
- 1.82
Funders
- Japan Agency for Medical Research and Development
- Ministry of Education, Culture, Sports, Science and Technology
- King Abdullah University of Science and Technology
- King Fahad Medical City
- King Salman Center for Disability Research
- Japan Society for the Promotion of Science
- Japan Science and Technology Agency
- Dalian Institute of Chemical Physics
- Institute of Genetics
- National Bioscience Database Center