Fig. 2: Comparison of Harukei-3 and DHL92 genome references.

a A circos plot comparing Harukei-3 and DHL92 genomes. Frequencies of physical gap [i], transposable elements [iii], predicted genes [iv], genes absent in either genome [vii], candidate genes for copy number variation (CNV) and presence/absence polymorphism (PAP) [viii], orthologue and homologue partners [ix] are drawn in the plot together with the chromosome [ii], heatmaps of gene count with FPKM (Fragments Per Kilobase of exon per Million mapped fragments; gene expression levels) ≥ 0.1 [v] or averaged FPKM [vi] in the tissue-wide transcriptome dataset shown in Fig. 3. Orthologous or homologous gene partners are shown by links in the center of the plot (also shown in the right panels). One-to-one orthologous gene partners (24,747 links) or homologous partners (1317 links) are indicated by blue and gray lines in which blue line indicate that genes are located at the same direction while gray lines indicate the opposite direction. Purple, red, and orange links indicate 483 tandem duplication CNVs, 720 non-tandem CNVs and PAPs, and 948 genes that are unanchored in either genome, respectively. b Gene ID nomenclature in the Harukei-3 ver. 1.41 genome reference. Consensus gene ID that starts with “MELO3C” string are attached to 24,758 Harukei-3 genes that have one-to-one orthologues in DHL92 genome.