Soybean (Glycine max), known in Japanese as daizu, is one of the most important crops in the world. Its production is closely linked to food security, as soybeans are used not only for oil production but also as a major source of livestock feed. In Japan, several traditional soy-based foods such as miso, tofu, natto, and edamame are widely consumed. In Japanese soybean breeding, traits such as large seed size, round seed shape, and high protein content have been important targets. The NARO institute has been conducting genomics research on several standard Japanese cultivars, including 'Enrei' and 'Fukuyutaka'. In 2015, a contig dataset of the 'Enrei' cultivar was published using the Roche 454 platform (Enrei V2). To further advance data-driven breeding and functional genomics research in soybean, we have completely updated the 'Enrei' genome reference by integrating Oxford Nanopore long-read sequencing, BioNano optical mapping, and Hi-C data. This new reference, designated as Enrei V3, contains around 59,000 protein-coding genes and achieves a complete BUSCO5 score of 99.8%. The primary goal of the 'Daizu-net' web database is to provide comprehensive information on the Enrei V3 reference, including sequence data for each gene and supporting evidence for the consensus gene IDs. Currently, several web applications are available, as listed below.
contact: sh-daizunet-public-info [-at-] naro.go.jp
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✿ Our paper has been published. Please cite the following paper:
- Yano et al. (2025) Nature Genetics 57, 973-985. The genomic landscape of gene-level structural variations in Japanese and global soybean Glycine max cultivars.
DOI: 10.1038/s41588-025-02113-5
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[18th Jan, 2024] Added EST alignment to Enrei v3.31 (GFF=3.32) and Wm82 508v4.
[8th June, 2023] Dotplot view is available for 41 genome assemblies including 7 NARO genomes [based on Enrei v3.31 (GFF=3.32)].
*Example of dotplot view between Enrei_ver3.31 and Wm82 508v4.
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[23th Jul, 2025] Resequencing dataset of 462 G.max lines including the NARO core collection, JP cultivars, and publicly available datasets is available.
*Depth data is inserted only for Enrei v3.31 reference. The 462 dataset includes redundant entries for the cultivar 'Enrei'.
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[5th Dec, 2025] Several bugs fixed.
[11th Nov, 2025] App modified to improve search speed.
[23th Jul, 2025] Resequencing dataset of 462 G.max lines including the NARO core collection, JP cultivars, and publicly available datasets is available.
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[9th Jan, 2024] Updated datasets based on Enrei v3.31 (GFF=3.32).
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[9th Jan, 2024] Updated datasets based on Enrei v3.31 (GFF=3.32).
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[23th May, 2026] Updated ORF finder.
[9th Jan, 2024] Updated datasets based on Enrei v3.31 (GFF=3.32).
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[9th Jab, 2024] Bugs fixed and updated datasets based on Enrei v3.31 (GFF=3.32).
[18th Aug, 2023] Updated gene-level synteny view function.
[8th July, 2023] Updated multi-genome synteny view function.
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*preview version, distict research project (external server)
[13th Apr, 2023] Co-expression dataset of 44 RNA-seq (22 tissues, Enrei and Williams82) based on Enrei v3.31 (GFF=3.32).
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