Figures (3)  Tables (2)
    • Figure 1. 

      Comparison of the UQ Nipponbare genome with previously published reference genome assembly IRGSP.1.0 Nipponbare. (a), (b) For UQ Nipponbare all the chromosome sizes are larger and most include telomeres as compared to IRGSP.1.0 Nipponbare. (c) Whole genome dot plot of UQ Nipponbare genome vs IRGSP.1.0 Nipponbare.

    • Figure 2. 

      Sequence collinearity and structural variants, including inversions, translocations, duplications, and non-aligning regions, were analysed between the UQ Nipponbare genome assembly and the IRGSP-1.0-Nipponbare genome assembly. The two assemblies were aligned using minimap2, and the resulting BAM file was indexed with samtools. Detection of structural variations between these two genomes was performed using SyRI[2628]. The non-aligning regions of chromosomes 1 and 11 are highlighted in the bottom section of the figure.

    • Figure 3. 

      Sequence collinearity and structural variants, including inversions, translocations, duplications, and non-aligning regions, were examined between the UQ Nipponbare haplotype 1 genome assembly and the UQ Nipponbare haplotype 2 genome assembly. The same method used in Fig. 2 was used for this analysis.

    • UQ_Nip-collapsedUQ_Nip-Hap1UQ_Nip-Hap2
      Total assembly size381,317,026379,234,557348,265,595
      Complete BUSCOs (%)99.30%98.90%94.90%
      Total scaffold number121212
      Scaffold N5030,712,25230,691,51229,307,860
      Scaffold L50666
      Largest scaffold43,960,27743,881,44437,312,016
      GC content (%)444443

      Table 1. 

      Statistics for the UQ Nipponbare haplotype resolved genome assembly.

    • UQ_Nip-Collapsed-AssemblyUQ_Nip-Hap1UQ_Nip-Hap2
      ChrSizeTelomereChrSizeTelomeresChrSizeTelomeres
      OSUQ0143,960,2772OSUQ01-hap1-0143,881,4442OSUQ01-hap2-0137,312,0162
      OSUQ0236,506,0492OSUQ02-hap1-0236,408,5622OSUQ02-hap2-0233,128,2682
      OSUQ0337,404,1302OSUQ03-hap1-0337,357,6162OSUQ03-hap2-0335,934,9622
      OSUQ0436,083,2202OSUQ04-hap1-0435,866,3582OSUQ04-hap2-0433,298,2062
      OSUQ0530,417,6982OSUQ05-hap1-0530,178,9462OSUQ05-hap2-0524,819,4152
      OSUQ0632,132,6402OSUQ06-hap1-0632,049,8322OSUQ06-hap2-0632,067,1052
      OSUQ0729,813,5882OSUQ07-hap1-0729,708,4132OSUQ07-hap2-0728,849,9532
      OSUQ0828,607,5462OSUQ08-hap1-0828,566,8762OSUQ08-hap2-0826,254,2481
      OSUQ0923,461,7441OSUQ09-hap1-0923,221,905OSUQ09-hap2-0921,159,1881
      OSUQ1023,948,7512OSUQ10-hap1-1023,192,9842OSUQ10-hap2-1021,409,9762
      OSUQ1130,712,2522OSUQ11-hap1-1130,691,5122OSUQ11-hap2-1129,307,8601
      OSUQ1228,269,1312OSUQ12-hap1-1228,110,1092OSUQ12-hap2-1224,724,3982

      Table 2. 

      UQ Nipponbare haplotype resolved genome assembly chromosomes sizes and telomere numbers.