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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.
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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[26−28]. The non-aligning regions of chromosomes 1 and 11 are highlighted in the bottom section of the figure.
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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.
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UQ_Nip-collapsed UQ_Nip-Hap1 UQ_Nip-Hap2 Total assembly size 381,317,026 379,234,557 348,265,595 Complete BUSCOs (%) 99.30% 98.90% 94.90% Total scaffold number 12 12 12 Scaffold N50 30,712,252 30,691,512 29,307,860 Scaffold L50 6 6 6 Largest scaffold 43,960,277 43,881,444 37,312,016 GC content (%) 44 44 43 Table 1.
Statistics for the UQ Nipponbare haplotype resolved genome assembly.
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UQ_Nip-Collapsed-Assembly UQ_Nip-Hap1 UQ_Nip-Hap2 Chr Size Telomere Chr Size Telomeres Chr Size Telomeres OSUQ01 43,960,277 2 OSUQ01-hap1-01 43,881,444 2 OSUQ01-hap2-01 37,312,016 2 OSUQ02 36,506,049 2 OSUQ02-hap1-02 36,408,562 2 OSUQ02-hap2-02 33,128,268 2 OSUQ03 37,404,130 2 OSUQ03-hap1-03 37,357,616 2 OSUQ03-hap2-03 35,934,962 2 OSUQ04 36,083,220 2 OSUQ04-hap1-04 35,866,358 2 OSUQ04-hap2-04 33,298,206 2 OSUQ05 30,417,698 2 OSUQ05-hap1-05 30,178,946 2 OSUQ05-hap2-05 24,819,415 2 OSUQ06 32,132,640 2 OSUQ06-hap1-06 32,049,832 2 OSUQ06-hap2-06 32,067,105 2 OSUQ07 29,813,588 2 OSUQ07-hap1-07 29,708,413 2 OSUQ07-hap2-07 28,849,953 2 OSUQ08 28,607,546 2 OSUQ08-hap1-08 28,566,876 2 OSUQ08-hap2-08 26,254,248 1 OSUQ09 23,461,744 1 OSUQ09-hap1-09 23,221,905 OSUQ09-hap2-09 21,159,188 1 OSUQ10 23,948,751 2 OSUQ10-hap1-10 23,192,984 2 OSUQ10-hap2-10 21,409,976 2 OSUQ11 30,712,252 2 OSUQ11-hap1-11 30,691,512 2 OSUQ11-hap2-11 29,307,860 1 OSUQ12 28,269,131 2 OSUQ12-hap1-12 28,110,109 2 OSUQ12-hap2-12 24,724,398 2 Table 2.
UQ Nipponbare haplotype resolved genome assembly chromosomes sizes and telomere numbers.
Figures
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Tables
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