2025-08-13 国立国際医療研究所,九州大学,東京大学,ライフサイエンス統合データベースセンター,生命情報・DDBJセンター
<関連情報>
- https://www.ri.jihs.go.jp/topics/release/2025/202508121800.html
- https://www.ri.jihs.go.jp/topics/release/2025/pdf/20250812_05.pdf
- https://www.nature.com/articles/s41597-025-05652-y
日本とサウジアラビアの人口集団の段階的ゲノムアセンブリとパンゲノムグラフ Phased genome assemblies and pangenome graphs of human populations of Japan and Saudi Arabia
Maxat Kulmanov,Saeideh Ashouri,Yang Liu,Marwa Abdelhakim,Ebtehal Alsolme,Masao Nagasaki,Yasuyuki Ohkawa,Yutaka Suzuki,Rund Tawfiq,Katsushi Tokunaga,Toshiaki Katayama,Malak S. Abedalthagafi,Robert Hoehndorf & Yosuke Kawai
Scientific Reports Published:12 August 2025
DOI:https://doi.org/10.1038/s41597-025-05652-y
Abstract
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.
