[Daizu-net] Data download

✿ 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

Data download

G.max NARO standard genome reference (de novo assembly) (28th, Jun, 2024)

[download] Enrei v3.31 pseudomolecule assembly (fasta) *assembled by Oxford Nanoore + BioNano saphyr + Hi-C

[download] Enrei v3.32 annotation, original gene ID (GFF3) *gene prediction by Oxford Nanoore + EVM (BRAKER2, augustus, genome threader, stringtie)

[download] Enrei v3.32 annotation, consensus gene ID (GFF3) *Williams Glyma gene ID is attached if 1-to-1 paired orthologue was found.

*GFF has been updated to v3.32. Gene ID strings of 27 genes were fixed without changing their genomic positions and exon/intron structures.
*No changes in DNA sequences between v3.30 and v3.31. Prefix 'Enrei331_chr' is attached to the chrosomome sequence names in v3.31.

G.max NARO genome references (reference-guided) (28th, Jun, 2024)

- Japanese cultivars and landraces -

[download] Fukuyutaka v3.12 pseudomolecule assembly (fasta) [1]

[download] Fukuyutaka v3.12 annotation, original gene ID (GFF3) [2]

[download] Himeshirazu v3.02 pseudomolecule assembly (fasta) [3]

[download] Himeshirazu v3.02 annotation, original gene ID (GFF3) [2]

[download] Kosuzu v3.01 pseudomolecule assembly (fasta) [3]

[download] Kosuzu v3.01 annotation, original gene ID (GFF3) [2]

[download] Miyagishirome v3.01 pseudomolecule assembly (fasta) [3]

[download] Miyagishirome v3.01 annotation, original gene ID (GFF3) [2]

[download] Ooyachi2 v3.03 pseudomolecule assembly (fasta) [3]

[download] Ooyachi2 v3.03 annotation, original gene ID (GFF3) [2]

[download] Tanba v3.02 pseudomolecule assembly (fasta) [3]

[download] Tanba v3.02 annotation, original gene ID (GFF3) [2]

- others -

[download] Harosoy v3.01 pseudomolecule assembly (fasta) [3]

[download] Harosoy v3.01 annotation, original gene ID (GFF3) [2]

[download] Jack v3.01 pseudomolecule assembly (fasta) [3]

[download] Jack v3.01 annotation, original gene ID (GFF3) [2]

[download] Peking v3.01 pseudomolecule assembly (fasta) [3]

[download] Peking v3.01 annotation, original gene ID (GFF3) [2]

[download] UA4805 v3.01 pseudomolecule assembly (fasta) [1]

[download] UA4805 v3.01 annotation, original gene ID (GFF3) [2]

  [1] assembled by Oxford Nanoore + BioNano saphyr + ragtag
  [2] gene prediction by Oxford Nanoore + EVM (BRAKER3, augustus, genome threader, stringtie)
  [3] assembled by Oxford Nanoore + ragtag
  *These data do not include organella sequences.

Raw sequence data deposited in public database (28th, Oct, 2023)

[LINK] Nanopore, Illumina, Bionano map, and Proximo Hi-C dataset of Enrei and Fukuyutaka (NCBI PRJNA935991)

[LINK] Nanopore and Illumina dataset of seven soybean accessions (Himeshirazu, Kosuzu, Miyagishirome, Tanba, Harosoy, Jack, and Peking) (NCBI PRJNA1029916)

[LINK] Tissue-wide RNA-seq in Enrei and Williams 82 (total 44 samples) (NCBI PRJNA934964)

Pipeline and script

[LINK] Asm2sv, a pipeline for assembly-based comparative genomics study

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