Fig. 1

Quality assessment of the LC2 v1.0 genome assembly. A The plant with fruit of A. arguta cv. ‘Longcheng No.2’. B Comparison of the amount of distinct K-mers absent and copy number variation between LC2 v1.0 assembly and raw HiFi reads. The plots are colored to illustrate the times of specific K-mers referred from the reads appeared in the assembly. The blackness represents K-mers missing from the assembly, while color of red, purple, green, blue, yellow or orange represents K-mers that appear 1, 2, 3, 4, 5 or ≥ 6 times in the assembly, respectively. C Heatmap displaying Hi-C interacting signals of LC2 v1.0 chromosomes. Each homologous group contains four chromosomes. D Collinearity between the four haplotypes of LC2 v1.0 and HY4P. HY4P was used for adjusting the orientation of LC2 v1.0 chromosomes. E Genome BUSCO and gene BUSCO assessments exhibiting proportions classified as categories of complete and single-copy (S, green), complete and duplicated (D, blue), fragmented (F, yellow), and missing (M, pink). F Distribution of LAI scores among the assemblies of four haplotypes of LC2 v1.0. G Genomic features of the four haplotypes of LC2 v1.0. Tracks from outside to inside are chromosome identifiers (Chr), gene density (Gene), guanine-cytosine (GC) content, repeat density (Repeats), InDel density (InDel) and SNP density (SNP). All statistics were computed for windows of 500 Kb