Fig. 1: Nanopore-based genome references for Japanese and other soybean lines.
a, Phylogenetic tree of 462 worldwide soybean cultivars and varieties. The analysis was conducted using a resequencing (SNPs and short indels) dataset based on the Williams 82 Gmax_508 v4.0 reference. One wild soybean accession was used as an outgroup taxon. b, Principal component analysis of 462 soybeans based on the dataset used in a. c, Genome assembly and annotation statistics in newly constructed genomes. The ‘Num. gaps’ values indicate the number of gaps with ≥100 bp on 20 chromosomes. BUSCO5 benchmark28 was used to evaluate the completeness of the protein sequence datasets. chrs., chromosomes; num., number; seqs., sequences. d, Circos plots comparing the Enrei and Williams 82 Gmax_508 genome references. One-to-one orthologous gene partners (48,518 links) are indicated by blue (genes are located in the same direction) and gray (genes are located in the opposite direction) lines. Purple, red and orange links indicate 719 tandem copy number variations (CNV), 1,944 other SV types and 114 genes that were unanchored to either genome, respectively. e, Gene ID nomenclature in the Enrei v3.31 genome reference. The consensus gene ID started with a ‘Glyma.’ string attached to Enrei genes that have one-to-one orthologs in either version of Williams 82 v4.0, v2.0 or v1.0 (see also Supplementary Fig. 5).
