Fig. 1

Overview of the assembly quality and characteristics of the HFTH1 genome. a Regenerated plantlets derived from Hanfu anther culture and the dramatic changes between the HFTH1 phenotype and the heterozygous donor (HFP) genotype. b Homozygosity analysis of chromosome 01 of HFTH1 and HFP using simple sequence repeats (SSRs, the results of the analysis of all chromosomes are shown in Supplementary Fig. 1). c Counts of SNPs detected in the GDDH13 and HFTH1 genomes. SNPs were detected using Illumina reads from the same individual that was used for the assembly. The heterozygous SNP (red) represents the heterozygosity of a genome and the homozygous SNP (blue) represents the potential error for an assembly. d Distribution of the contig length in the assemblies of Arabidopsis (TAIR10), Nipponbare (RGAP7), HFTH1 and GDDH13. Each contig size (y-axis) represents the minimum contig size that covered the cumulative percentage of the assembly (x-axis) after the assembled contigs were sorted from the largest to the smallest. e Hi–C interactions among 17 chromosomes with a 100-kb resolution. Strong interactions are indicated in dark red and weak interactions are indicated in yellow. f Circular diagram depicting the characteristics of the HFTH1 genome. The tracks from outer to inner circles indicate the following: a chromosomes (Chr.), gaps and telomeres, the black regions at the end of each chromosome represent assembled the telomere sequences and the grey regions represent gap regions; b gene density (window size of 1 Mb); c repeat density (window size of 1 Mb); d Copia-7; e Golden Delicious shared SNPs (window size of 500 kb)